I'm very much in the evolution/science camp of this issue, but something has been floating around in my mind vaguely for a while now and it relates to what what we mean by science at all.
We in the science camp more or less know the big answer behind each question; evolution did it. So when some creationist triumphantly claims that evolution doesn't explain how a squirrels knee joint could have come to be, we don't freak out. The answer is something like, well we haven't specifically studied that yet, but we're confident that the answer will fit with the evolution story, just like everything else has.
This is all fine, but the trouble is that it can very easily look like, or actually become (in some cases I'm sure) a story that's made up specifically to fit with your theory, which is bad.
In reality, there's bound to be some of this going on.
The thing is though that sciency types often gripe at religious types for exactly this.
Religious people also know the big answer which lies behind all the questions. God did it. People like me then ask why evil exists if God is omnipotent and all loving. The religious can just say, well that's an interesting problem, but the answer will fit with the God story, just like everything else has. Here's a nice theodicy!
Sure, the story looks suspiciously like we're arguing for a specific conclusion from the start, which may not even consider other possible explanations, but how is this different to those evolution types? Huh?
Added: A reader commented to me that this was another of my anti-religious posts. Weird how different things can seem to different people...