The only tracks I normally ever skip are those horrible skits and interlude tracks. I really can't wait for the day when every artist on the planet suddenly realizes that putting non-musical interludes on your album is really fucking annoying after the 2nd listen or so and completely ruins the flow of the music (example: Tool - Aenima).
Oh, and tracks that are padded with 10 minutes of silence after which it starts playing a "hidden track" (ooh they are always so hard to find!). That's really annoying as well and I usually skip that too. Then there's ofcourse the albums that just end with white noise/beeping (SYL - Alien, Tool - Lateralus, etc.). I skip those too.
Basically I only skip stuff that I do not consider to be music.