My personal fave: Amy Poehler's "I thought you were SPECIAL!" scene from WET HOT AMERICAN SUMMER.
Near the beginning of that hour of deleted footage on the second INLAND EMPIRE dvd, there's a chunk lasting 15 or 20 minutes that's easily better than most of what made it into the film. Particularly during a creepy scene in which Laura Dern watches her husband get into bed and turn out the light, but only a moment later when she calls his name he doesn't seem to be in the room anymore.
Also, there are at least 2 deleted scenes from STUCK ON YOU (Greg Kinnear's funny/sad "Well, what have we here?" post-surgery scene, when habit finds him whispering to a brother that isn't there, and the fishing scene near the end, which is just plain poignant) that really shouldn't have been dumped in favor of more (yawn) Cher jokes.