I think all three were excellent in their times as Megatron, but I gotta give the nod to David Kaye. I grew up with him, and there is something about him that I just love. Don't get me wrong, Welker was a damn fine Megatron, and Weaving did a great job (in the few lines he actually got) in the movie, but I just prefer David Kaye.
Like someone else also made reference too, this quote from Beast Wars was just great:
"Say goodbye to the universe, Maximals. The future has changed, yesss. The Autobots lose. Evil triumphs. And you, you NO LONGER EXIST!"