This is a much tougher topic, but I can remember a few brilliant movie scenes that I was shocked that were cut. Thankfully, we have DVD's....
1) In High Fidelity, Cusacks character goes to the house of a lady (played by Beverly D'Angelo) who tries to sell her husbands record collection and Cusack won't buy because she has way undervalued the records. Her husband left her and she want's to spite him by dumping them, but Cusack won't do it. A great scene. His reaction to the original Sex Pisols and Clash 45's is awesome. A brilliant scene that I wish was included
2) There are two scenes from Bull Durham that didn't make it - one where Nuke is getting shelled and Crash and the coach go to talk to him and the coach says "relax, you're throwing too hard. Crash, how's he look?" and crash goes "I don't know, I haven't caught one yet." Another scene was changed - originally the "Lollygagging" scene was supposed to involve the Figure Skating girls, but they changed it. Both were funny though.