* There was 1 great but not very subtle Star Wars reference. At one point, not sure where, Indy shouts 'I've got a bad feeling about this'. The line is used in every SW film, so a nice nod I guess.
* Of course the movie was situated in the 50's for a reason, but they didn't chose to make Shia a greaser for no reason. I think most of that came from Lucas' simply being a big fan of that certain time, mainly referenced in 'American Graffiti', where Harrison Ford had a role as well.
* Of course there was the whole Mutt hat/jacket/bike reference to Marlon Brando and the Wild One. Gotta love that bike.
* The scene where they're hanging in that tree over the water reminded me a lot of Jurassic Park from a certain angle. Not an obvious nod, but I can imagine Spielberg had a laugh about it.
* I hope everyone noticed, but for those who didn't for some reason, the big statue the car hits is of course Marcus Brody.
* I'm fairly sure the UFO in the end had some resemblance to the UFO in Close Encounters, apart from being .. round. Might not be a reference though.
* Remember Indy's 'last words' when he first met Spalko? 'I like Ike'. It said the same thing on the bomb we saw afterwards.
Check out the following clip to see what that's about:
http://www.youtube.com/watch?v=va5Btg4kkUE