I'm going to be a rebel and say Infernal Machine. It still had the puzzle and adventure elements of Fate of Atlantis but with a gigantic 3D environment to explore with some wonderful set-pieces. Yes it's a bit slow and the lack of proper mouse support is criminal, but I still think it's the best. The story, featuring the only post-WW2 Indy until Indy IV comes out, is pretty cool too.
And you can save anywhere, unlike Emperor's "That Damn Shark Got Me AGAIN" Tomb.
You know, I was thinking of a big discussion at some point about this topic, maybe for MixnMojo's planned 'Indy Month 2' in May.