Transition from primitive jawless fish to sharks, skates, and rays:

o Cladoselachians (e.g., Cladoselache).
o Hybodonts (e.g. Hybodus)
o Heterodonts (e.g. Heterodontus)
o Hexanchids (e.g. Chlamydoselache)

Transition from primitive bony fish to holostean fish:

o Palaeoniscoids (e.g. Cheirolepis); living chondrosteans such as Polypterus and Calamoichthys, and also the living acipenseroid chondrosteans such as sturgeons and paddlefishes.
o Primitive holosteans such as Semionotus.

Transition from holostean fish to advanced teleost fish:

o Leptolepidomorphs, esp. Leptolepis, an excellent holostean-teleost intermediate
o Elopomorphs, both fossil and living (tarpons, eels)
o Clupeomorphs (e.g. Diplomystus)
o Osteoglossomorphs (e.g. Portheus)
o Protacanthopterygians

Transition from primitive bony fish to amphibians:

o Paleoniscoids again (e.g. Cheirolepis)
o Osteolepis -- one of the earliest crossopterygian lobe-finned fishes, still sharing some characters with the lungfish (the other group of lobe-finned fish). Had paired fins with a leg-like arrangement of bones, and had an early-amphibian-like skull and teeth.
o Eusthenopteron (and other rhipidistian crossopterygian fish) -- intermediate between early crossopterygian fish and the earliest amphibians. Skull very amphibian-like. Strong amphibian-like backbone. Fins very like early amphibian feet.
o Icthyostegids (such as Icthyostega and Icthyostegopsis) -- Terrestrial amphibians with many of Eusthenopteron's fish features (e.g., the fin rays of the tail were retained). Some debate about whether Icthyostega should be considered a fish or an amphibian; it is an excellent transitional fossil.
o Labyrinthodonts (e.g., Pholidogaster, Pteroplax) -- still have some icthyostegid features, but have lost many of the fish features (e.g., the fin rays are gone, vertebrae are stronger and interlocking, the nasal passage for air intake is well defined.)

Transition from amphibians to reptiles:

o Seymouriamorph labyrinthodonts (e.g. Seymouria) -- classic labyrinthodont skull and teeth, with reptilian vertebrae, pelvis, humerus, and digits; amphibian ankle.
o Cotylosaurs (e.g. Hylonomus, Limnoscelis) -- slightly amphibian skull (e.g. with amphibian-type pineal opening), with rest of skeleton classically reptilian.
o The cotylosaurs gave rise to many reptile groups of tremendous variety. I won't go into the transitions from cotylosaurs to the advanced anapsid reptiles (turtles and possibly mesosaurs), to the euryapsid reptiles (icthyosaurs, plesiosaurs, and others), or to the lepidosaurs (eosuchians, lizards, snakes, and the tuatara), or to most of the dinosaurs, since I don't have infinite time. Instead I'll concentrate on the synapsid reptiles (which gave rise to mammals) and the archosaur reptiles (which gave rise to birds).

Transition from reptiles to mammals:

o Pelycosaur synapsids -- classic reptilian skeleton, intermediate between the cotylosaurs (the earliest reptiles) and the therapsids (see next)
o Therapsids (e.g. Dimetrodon) -- the numerous therapsid fossils show gradual transitions from reptilian features to mammalian features. For example: the hard palate forms, the teeth differentiate, the occipital condyle on the base of the skull doubles, the ribs become restricted to the chest instead of extending down the whole body, the legs become "pulled in" instead of sprawled out, the ilium (major bone of the hip) expands forward.
o Cynodont theriodonts (e.g. Cynognathus) -- very mammal-like reptiles. Or is that reptile-like mammals? Highly differentiated teeth (a classic mammalian feature), with accessory cusps on cheek teeth; strongly differentiated vertebral column (with distinct types of vertebrae for the neck, chest, abdomen, pelvis, and tail -- very mammalian), mammalian scapula, mammalian limbs, mammalian digits (e.g. reduction of number of bones in the first digit). But, still has unmistakably reptilian jaw joint.
o Tritilodont theriodonts (e.g. Tritylodon, Bienotherium) -- skull even more mammalian (e.g. advanced zygomatic arches). Still has reptilian jaw joint.
o Ictidosaur theriodonts (e.g. Diarthrognathus) -- has all the mammalian features of the tritilodonts, and has a double jaw joint; both the reptilian jaw joint and the mammalian jaw joint were present, side-by-side, in Diarthrognathus's skull. A really stunning transitional fossil.
o Morganucodonts (e.g. Morganucodon) -- early mammals. Double jaw joint, but now the mammalian joint is dominant (the reptilian joint bones are beginning to move inward; in modern mammals these are the bones of the middle ear).
o Eupantotheres (e.g. Amphitherium) -- these mammals begin to show the complex molar cusp patterns characteristic of modern marsupials and eutherians (placental mammals). Mammalian jaw joint.
o Proteutherians (e.g. Zalambdalestes) -- small, early insectivores with molars intermediate between eupantothere molars and modern eutherian molars.
o Those wondering how egg-laying reptiles could make the transition to placental mammals may wish to study the reproductive biology of the monotremes (egg-laying mammals) and the marsupials. The monotremes in particular could almost be considered "living transitional fossils". [see Peter Lamb's suggested marsupial references at end]

Transition from reptiles to birds:

o Lisboasaurus estesi and other "troodontid dinosaur-birds" -- a bird-like reptile with very bird-like teeth (that is, teeth very like those of early toothed birds [modern birds have no teeth]). May not have been a direct ancestor; may have been a "cousin" of the birds instead.
o Protoavis -- this is a highly controversial fossil that may or may not be an extremely early bird. Not enough of the fossil was recovered to determine if it is definitely related to the birds, or not. I mention it in case people have heard about it recently.
o Archeopteryx -- reptilian vertebrae, pelvis, tail, skull, teeth, digits, claws, sternum. Avian furcula (wishbone, for attachment of flight muscles), forelimbs, and lift-producing flight feathers. Archeopteryx could probably fly from tree to tree, but couldn't take off from the ground, since it lacked a keeled breastbone (for attachment of large flight muscles) and had a weak shoulder (relative to modern birds).
o "Chinese bird" [I don't know what name was given to this fossil] -- A fossil dating from 10-15 million years after Archeopteryx. Bird-like claws on the toes, flight-specialized shoulders, fair-sized sternal keel (modern birds usually have large sternal keel); also has reptilian stomach ribs, reptilian unfused hand bones, & reptilian pelvis. This bird has a fused tail ("pygostyle"), but I don't know how long it was, or if it was all fused or just part of it was fused.
o "Las Hoyas bird" [I don't know what name was given to this fossil] -- This fossil dates from 20-30 m.y. after Archeopteryx. It still has reptilian pelvis & legs, with bird-like shoulder. Tail is medium-length with a fused tip (Archeopteryx had long, unfused tail; modern birds have short, fused tail). Fossil down feather was found with the Las Hoyas bird.
o Toothed Cretaceous birds, e.g. Hesperornis and Ichthyornis. Skeleton further modified for flight (fusion of pelvis bones, fusion of hand bones, short & fused tail). Still had true socketed teeth, which are missing in modern birds.
o [note: a classic study of chicken embryos showed that chicken bills can be induced to develop teeth, indicating that chickens (and perhaps other modern birds) still retain the genes for making teeth.]

Now, on to some of the classes of mammals.

Transitional fossils from early eutherian mammals to primates:

o Early primates -- paromomyids, carpolestids, plesiadapids. Lemur-like clawed primates with generalized nails.
o Notharctus, an early Eocene lemur
o Parapithecus, a small Old World monkey (Oligocene)
o Propliopithecus, a small primate intermediate between Parapithecus and the more recent O.W. monkeys. Has several ape-like characters.
o Aegyptopithecus, an early ape.
o Limnopithecus, a later ape showing similarities to the modern gibbons.
o Dryopithecus, a later ape showing similarities to the non-gibbon apes.
o Ramapithecus, a dryopithecine-like ape showing similarities to the hominids but now thought to be an orang ancestor.
o Australopithecus spp., early hominids. Bipedal.
o Homo habilis.
o Homo erectus. Numerous fossils across the Old World.
o Homo sapiens sapiens. This is us. (NB: "Cro-magnon man" belongs here too. Cro-magnons were a specific population of modern humans.)
o Homo sapiens neanderthalensis (not on the direct line to H. sapiens sapiens, but worth mentioning).
o [I haven't described these fossils in detail because they're fairly well covered in any intro biology text, or in any of several good general- interest books on human evolution.]

Transitional fossils from early eutherian mammals to rodents:

o Paramyids, e.g. Paramys -- early "primitive" rodent
o Paleocastor -- transitional from paramyids to beavers
o [yick. I was going to summarize rodent fossils but Paramys and its friends gave rise to 5 enormous and very diverse groups of rodents, with about ten zillion fossils. Never mind.]

Transitional fossils among the cetaceans (whales & dolphins):

o Pakicetus -- the oldest fossil whale known. Only the skull was found. It is a distinct whale skull, but with nostrils in the position of a land animal (tip of snout). The ears were partially modified for hearing under water. This fossil was found in association with fossils of land mammals, suggesting this early whale maybe could walk on land.
o Basilosaurus isis -- a recently discovered "legged" whale from the Eocene (after Pakicetus). Had hind feet with 3 toes and a tiny remnant of the 2nd toe (the big toe is totally missing). The legs were small and must have been useless for locomotion, but were specialized for swinging forward into a locked straddle position -- probably an aid to copulation for this long-bodied, serpentine whale.
o Archaeocetes (e.g. Protocetus, Eocetus) -- have lost hind legs entirely, but retain "primitive whale" skull and teeth, with forward nostrils.
o Squalodonts (e.g. Prosqualodon) -- whale-like skull with dorsal nostrils (blowhole), still with un-whale-like teeth.
o Kentriodon, an early toothed whale with whale-like teeth.
o Mesocetus, an early whalebone whale
o [note: very rarely a modern whale is found with tiny hind legs, showing that some whales still retain the genes for making hind legs.]

Transitional fossils from early eutherian mammals to the carnivores:

o Miacids (e.g. Viverravus and Miacis) -- small weasel-like animals with very carnivore-like teeth, esp. the carnassial teeth.
o Arctoids (e.g. Cynodictis, Hesperocyon) -- intermediate between miacids and dogs. Limbs have elongated, carnassials are more specialized, braincase is larger.
o Cynodesmus, Tomarctus -- transitional fossils between arctoids and the modern dog genus Canis.
o Hemicyon, Ursavus -- heavy doglike fossils between the arctoids and the bears.
o Indarctos -- early bear. Carnassial teeth have no shearing action, molars are square, short tail, heavy limbs. Transitional to the modern genus Ursus.
o Phlaocyon -- a climbing carnivore with non-shearing carnassials, transitional from the arctoids to the procyonids (raccoons et al.)
Meanwhile back at the ranch,
o Plesictis, transitional between miacids (see above) and mustelids (weasels et al.)
o Stenoplesictis and Palaeoprionodon, early civets related to the miacids (see above)
o Tunguricits, transitional between early civets and modern civets
o Ictitherium, transitional between early civets to hyenas
o Proailurus, transitional from early civets to early cats
o Dinictis, transitional from early cats to modern "feline" cats
o Hoplophoneus, transitional from early cats to "saber-tooth" cats

Transitional fossils from early eutherians to hoofed animals:

o Arctocyonid condylarths -- insectivore-like small mammals with classic mammalian teeth and clawed feet.
o Mesonychid condylarths -- similar to the arctocyonids, but with blunt crushing-type cheek teeth, and flattened nails instead of claws.
o Late condylarths, e.g. Phenocodus -- a fair-sized animal with hoofs on each toe (all toes were present), a continuous series of crushing-type cheek teeth with herbivore-type cusps, and no collarbone (like modern hoofed animals).

Transitional fossils from early hoofed animals to perissodactyls:

o [Perissodactyls are animals with an odd number of toes; most of the weight is borne by the central 3rd toe. Horses, rhinos, tapirs.]
o Tetraclaeonodon -- a Paleocene condylarth showing perissodactyl-like teeth
o Hyracotherium -- the famous "dawn horse", an early perissodactyl, with more elongated digits and interlocking ankle bones, and slightly different tooth cusps, compared to to Tetraclaeonodon. A small, doggish animal with an arched back, short neck, and short snout; had 4 toes in front and 3 behind. Omnivore teeth.
o [The rest of horse evolution will be covered in an upcoming "horse fossils" post in a few weeks. To whet your appetite:]
o Orohippus -- small, 4/3 toed, developing browser tooth crests
o Epihippus -- small, 4/3 toed, good tooth crests, browser
o Epihippus (Duchesnehippus) -- a subgenus with Mesohippus-like teeth
o Mesohippus -- 3 toed on all feet, browser, slightly larger
o Miohippus -- 3 toed browser, slightly larger [gave rise to lots of successful three-toed browsers]
o Parahippus -- 3 toed browser/grazer, developing "spring foot"
o 'Parahippus' leonensis -- a Merychippus-like species of Parahippus
o 'Merychippus' gunteri -- a Parahippus-like species of Merychippus
o 'Merychippus' primus -- a more typical Merychippus, but still very like Parahippus.
o Merychippus -- 3 toed grazer, spring-footed, size of small pony (gave rise to tons of successful three-toed grazers)
o Merychippus (Protohippus) -- a subgenus of Merychippus developing Pliohippus-like teeth.
o Pliohippus & Dinohippus -- one-toed grazers, spring-footed
o Equus (Plesippus) -- like modern equines but teeth slightly simpler.
o Equus (Hippotigris), the modern 1-toed spring-footed grazing zebras.
o Equus (Equus), the modern 1-toed spring-footed grazing horses & donkeys. [note: very rarely a horse is born with small visible side toes, indicating that some horses retain the genes for side toes.]
o Hyrachyids -- transitional from perissodactyl-like condylarths to tapirs
o Heptodonts, e.g. Lophiodont -- a small horse-like tapir, transitional to modern tapirs
o Protapirus -- a probable descendent of Lophiodont, much like modern tapirs but without the flexible snout.
o Miotapirus -- an almost-modern tapir with a flexible snout, transitional between Protapirus and the modern Tapirus.
o Hyracodonts -- early "running rhinoceroses", transitional to modern rhinos
o Caenopus, a large, hornless, generalized rhino transitional between the hyracodonts and the various later groups of modern & extinct rhinos.

Transitional fossils from early hoofed animals to some of the artiodactyls (cloven-hoofed animals):

o Dichobunoids, e.g. Diacodexis, transitional between condylarths and all the artiodactyls (cloven-hoofed animals). Very condylarth-like but with a notably artiodactyl-like ankle.
o Propalaeochoerus, an early pig, transitional between Diacodexis and modern pigs.
o Protylopus, a small, short-necked, four-toed animal, transitional between dichobunoids and early camels. From here the camel lineage goes through Protomeryx, Procamelus, Pleauchenia, Lama (which are still alive; these are the llamas) and finally Camelus, the modern camels.
o Archeomeryx, a rabbit-sized, four-toed animal, transitional between the dichobunoids and the early deer. From here the deer lineage goes through Eumeryx, Paleomeryx and Blastomeryx, Dicrocerus (with antlers) and then a shmoo of successful groups that survive today as modern deer -- muntjacs, cervines, white-tail relatives, moose, reindeer, etc., etc.
o Palaeotragus, transitional between early artiodactyls and the okapi & giraffe. Actually the okapi hasn't changed much since Palaeotragus and is essentially a living Miocene giraffe. After Palaeotragus came Giraffa, with elongated legs & neck, and Sivatherium, large ox-like giraffes that almost survived to the present.

So, there's a partial list of transitional fossils.