A few of mine were already covered, but heres two I haven't seen mentioned yet:
Fixed scrolling - When I scroll down and it yanks me back up, or yanks me further down than where I actually scrolled to. This genuinely pisses me off. I stopped scrolling where I wanted to for a reason. Why are you forcing scroll positions? Why are certain positions "right" and not the rest?
Justified text - this is a minor annoyance, definitely not as severe as the scrolling one, but does put me off. It's simply hard for me to read due to the uneven spacing between words, and since each line ends at the same spot, its harder for me to keep track of which line I'm on (I have minor dyslexia).
And now to points other people covered!
Entrances:I find entrances (or whatever they're called) to often serve as no more than a roadblock which makes you look for the entrance button, then to wait again for the actual home page to load
If your site has content that warrants a warning but it's NOT a big part of your website overall, put that warning where the problematic content is! Not on the splash page!
long animations and transitions
I've definitely come across splash pages where I was hunting for the entrance link! I just want to see your site!! I have nothing against splash pages but I rarely actually read them ^^; and do find it silly when the warnings are more severe than the content. What really annoys me is entrance animation, like Skykristal said. I don't mind when I first visit a site, as I understand it is to give off a certain atmosphere and be an artistic touch, but I hate having to wait for the entrance animation every time I visit, it just gets old and annoying.
also, that flickering old TV effect that is overlayed onto the entire page, and there's no way to disable it!
Yes! I used to notice this more a few years ago, it seems the CRT effects people use are much more subtle and easier on the eyes now. The flickering and scrolling lines used to be bad.