Smashing Magazine has a great list of usability problems that are pervasive on some of the biggest sites.

Personally the whole “Popup to get content” drives me batty. You usually see this on full flash sites (movie sites are the worst), but it is used by lazy designers everywhere…

At the end of the article they have a nice checklist to keep in mind while you are designing new sites. Here is a slimmed down version…

1. You don’t use pop-ups.
2. You don’t change users’ window size.
3. You don’t use too small font sizes.
4. You don’t have unclear link text.
5. You don’t have dead links.
6. You have at most one animation per page.
7. You make it easy to contact you.
8. Your links open in the same window.

Definitely worth a look.