I am kind of surprised to see MI2 so highly ranked. I remember when it first came out it seemed like everyone HATED the ending and were ready to stage riots in the streets! I'm not sure MI3 ever really explained the ending to MI2, although I do think they made some jabs at it.
Anyway, the first three were all great. I went with 3 because of Murray, but 1 and 2 are the true classics that started it all. MI4 may not rank up there, but it one of the few 3D Adventure games I have ever been able to make it all the way through.
Only Day of the Tentacle comes close to the MI series.