There's a few very memorable dunks from my memory bank that I think have to be included in the Top 50, if not the top 10:
As much as I hate Duke, I don't know that I recall a better dunk than the alley-oop from Bobby Hurley to Grant Hill in the NCAA championship game (featured in the honorable mention of this compilation):
http://www.youtube.com/watch?v=bv1bXGEzEfQ
Also featured in the honorable mention category was Jerry Stackhouse's dunk over Duke that demands inclusion:
http://www.youtube.com/watch?v=Vv2b6zXBJiE&feature=related
From two Final Fours ago, Durrell Summers dunk over Stanley Robinson:
http://www.youtube.com/watch?v=KUPkO4x9guo
Jason Richardson was prolific during his short time at Michigan State, but I don't know that I'm seen a better in-game dunk then the one he put down against Arizona during his freshman season (starts at 3:37 of this clip):
http://www.youtube.com/watch?v=nwVv1MMiEUQ
No youtube found on this dunk, but from a Gopher fan perspective, the Sam Jacobson baseline drive and tomahawk throwdown against Iowa (at least that's how I remember it) deserves mention-and deserves a place on youtube.
The '88-89 Flyin' Illini (most memorable in my mind is Kenny Battle & Kendall Gill) could really light up the crowd, as evidenced in this clip:
http://www.youtube.com/watch?v=JK4iJ6RlWdM
A dunk I recall with great memories is from my college days (1992, 93?) when Oklahoma traveled to either Duke or UNC. They were down nearly double digits late in the game when Angelo Hamilton got a breakaway opportunity and rose up to slam down a 360 dunk-Vitale was speaking in tongues, he couldn't believe the craziness of doing that dunk at that moment in the game. Unfortunately no youtube video exists.
And historically speaking, you can't forget Lorenzo Charles. Doesn't garner beauty points, but when your dunk at the buzzer brings home a NCAA championship, it belongs on the list:
http://www.youtube.com/watch?v=puQvU4PBzhI