Growing up, The Last Crusade was my favorite because of the chemistry between actors, particularly Ford and Connery. The father-son theme really resonated with me.
But in recent years, I've come to regard Raiders as my favorite. I think this began a few years back when I did an Indy marathon, and by the time I got to TLC, I realized it was just a tad too humorous (when juxtaposed next to Raiders) and that I preferred the slightly more serious feel of the original film.
Though I liked Walter Donovan and his minions in TLC, I also felt the villains in Raiders were just a bit more menacing. Even the background Nazis in Raiders had a bit more of an air of menace than the ones in Last Crusade.
The difference in mood between the two is subtle and I did not even realize it until I did that marathon.
STILL...
I love Last Crusade. But Raiders is my current pick.
On a seperate note, I enjoy Temple of Doom tremendously too. I know it became fun for a while to pick on ToD, but it's still an awesome movie. I think part of the problem is that the Sankara Stones aren't as interesting as the Ark of the Covenant or Holy Grail. The threat is more local whereas the threat in the first and third films feels global, more of a "free world at stake" feel.
I quite enjoyed Kingdom of the Crystal Skull for what it is, but it does have quite a few problems. I can remember THE SECOND the movie started that the Paramount logo disintegrated into the weasel mound, I thought, "Oh, no. The Phantom Menace all over again." However, the movie still had a game Harrison Ford and had its moments of fun.