I don't have a single issue that stands out as being most important, but just for the purposes of example, here are a few things I could list -
1. Agree more with Obama on abortion
2. Don't like that I think taxes will be higher under Obama than McCain
3. I think Obama will get us out of Iraq faster, but I don't like what I think he's going to do to the overall military budget
4. Personality wise, McCain is a bit too hard line and stubborn for my taste. I also don't like all the reports of his violent temper. That stuff matters in foreign relations and dealings with congress.
5. I would probably prefer whoever Obama puts into the Supreme Court more than who McCain would nominate, particularly as far as keeping it balanced; I don't want it to swing either right or left too far, and since it's a bit right right now, it would only get further over under McCain.
6. This is going to sound strange, and I don't really understand it myself considering how much I hate deadlock, but I have an inherent dislike for a situation in which the President and Congress are both of the same party. It seems like Congressmen and Senators have been increasingly toeing the party line (at least before Bush's popularity really hit the crapper and people started turning on him), and I don't know that I like the thought of whoever is President just pushing everything they want through with no resistance. We already had that for most of Bush's presidency, and look at where that got us.
When it comes down to it, if I HAVE to vote for one of the two, I would probably vote Obama. I'll probably end up going third party as a protest vote against the two party system, though.