I'm a recent convert to evolution(within the past 45 days), and a large part of what led me to abandon Creationism was homologies like the bat's wing and the cytochrome c protein.
Keep in mind, as a devout creationist, I had no reason to base my decision to accept evolution on circular logic. The evidence simply fits evolution so perfectly that, as a man devoted to truth, I had no other choice but to change my beliefs on the issue.
Just as an example, I find cytochrome c an amazing protein because its structure of about 100 amino acids can be varied in an innumerable number of ways while still retaining it's essential function: the transport of a single electron.
As I understand it, nearly all animals use this protein, and it's structure does indeed vary greatly between different kinds of organisms. This fact isn't remarkable, however, until one considers that organisms which are closer on the evolutionary tree always have more similar cytochrome c than those which are farther apart. To me, the best explanation for this is common descent.
Of course, in order to come to this conclusion, I had to make a reasonable assumption that the cladistic data provided by cytochrome c analysis best fits evolution. This is not circular reasoning, it's normal human decision making.
IMHO, all it would take to shed some doubt on evolution would be to find a species of worm with a cytochrome c indentical to human cytochrome c. Nothing like this has ever been found. Homologies consistently confirm evolutionary theory. Such a find would definitely be "our rabbit in the Precambrain."