There’s abiogenesis, for starters. That’s a sciency hair’s breadth away from the spontaneous generation that Pasteur disproved. I know about the Miller experiment; last I heard, it’s obsolete.
Transitional fossils, or the lack thereof, are popular.
The ID crowd has what they call “irreducible complexity,” a concept that states (more or less) that there are some parts of organisms that could not be built up through random processes, and will probably cite the flagellum as such a part – the “watch in a box.”
I actually think that we have had some natural selection within species, post-Creation, but I don’t see that tying Man to a puddle of goo a zillion years gone.
Ultimately, I’ve decided that God said that He created the heavens and the Earth, and in a pretty short timeframe. My faith in general is based on the things that God has said, so what’s one more? It doesn’t seem likely that an almighty God would spend untold centuries worrying a protein together, then spend millions of years watching it wobble around, dying in droves, until it becomes Man. I call it the faith-first paradigm.
Which is not to say that I don’t think that science can never know the truth. I just think that it’s so caught up in evolution (which, admittedly, looks workable on paper) that they aren’t going to find it any time soon.
If it’s any help to you, there are a lot of atheists who don’t understand how evolution works, either.
And if you want to avoid condescension, don’t say things like, “I don’t mean to be condescending at all. I’m not saying all Christians don’t believe in evolution,” because your words are still saying that people who don’t believe in evolution are silly and that some Christians – the unsilly – do.
@DrBill There’s the six-day restriction; academic evolution takes a lot longer than that.