Harnessing powerful computational tools and applying Bayesian statistics, Theobald found that the evidence overwhelmingly supports UCA, regardless of horizontal gene transfer or multiple origins of life. Theobald said UCA is millions of times more probable than any theory of multiple independent ancestries.
What Theobald did not assume, however, was how far back these processes go in linking organisms genealogically. It is clear, say, that these processes are able to link the shared proteins found in all humans to each other genetically. But do the processes in these assumptions link humans to other animals? Do these processes link animals to other eukaryotes? Do these processes link eukaryotes to the other domains of life, bacteria and archaea? The answer to each of these questions turns out to be a resounding yes.
"A still more glorious dawn awaits Not a sunrise, but a galaxy rise A morning filled with 400 billion suns The rising of the milky way" -Carl Sagan
Some vestigial organs still have a purpose but this isn't the one it originally evolved to fill. Flightless birds which evolved from birds that could fly are a prime example of this as they can use them for stability or threat displays but cannot fly. Other vestigial organs serve little or no apparant purpose (As far as we can tell) but still develop. The appendix for example while not used to store cellulose digesting bacteria could act as a haven for our current digestive bacteria. A possible reason for the appendix remaining is that further reduction in its size may result in increased incidents of appencitis which can result from blockages in the appendix which are obviously more likely if it becomes smaller.
Good word, Asking, you've hit the nail on the head.
In my experience, this issue has centers largely around the Creationist misunderstanding of the term "vestigial". This term does not mean "useless", but rather "previously had a different use".
The most obvious vestigial structures, in my opinion, are the vestigial wings on flightless birds. These wings indisputably still have functions (heating, swimming, running acceleration, mating displays, etc), but they also were quite obviously meant to be used in flight (nearly all vestigial wings still clearly show the airfoil pattern required for flight, and their bone structures and muscles structures still show the same patterns as flying birds.
Thus, a vestigial structure is not a useless one, but rather one that once held a different function.