Hi, CosmicAtheist! Welcome to the zoo!
It's a multi-part answer, and I've only got a few minutes right now. 1) you are precisely right about "we still have a use for them but not the same use as our ancestors." Humans don't use the appendix for a digestion chamber, but we seem to use it a little as a reservoir of bacteria to repopulate the gut after a diarrhea attack. 2) Humans have a vomeronasal organ in their noses. We don't use them, though: there are no nerves attached to them, and the "accessory olfactory bulb" of the human brain forms
and then is resorbed during fetal development. Monkeys keep theirs and use them to sniff out mates. Gorillas and chimps, though, do like we do.
Maybe I can elaborate on this this weekend......