The two deleted scenes on Not Another Teen Movie. Not because there was anything that great about them, but they were the only easter eggs I discovered without outside help.
Some guy working on Hannibal took the tape from the time the director said “Cut,” to the time the camera stopped rolling and stitched it all together. He’s in a band and laid some music they’d written over it to make a pretty cool music video. It’s pretty awesome.
On the Return of the King EE there’s a great easter egg where Dominic Monaghan poses as a German journalist and does a phone interview with an unsuspecting Elijah Wood that’s pretty funny.
A friend of mine was the first to discover the one on Cast Away. It’s a snippet of audio from a Q&A session with the director. Someone in the audience asked him what was in the box Tom Hanks saved on the island all those years, and he answered, “A solar-powered waterproof satellite phone.” (paraphrase)