For me, Last Crusade is easily the best of the sequels. I love Ford and Connery's chemistry and their relationship adds a good heart to the film. They put them through scenes that are funny, serious and thrilling, thus giving the film an emotional heft the other sequels never match.
It also does the best job of combining emotional character bits, unlocking mysteries, thrilling action and international locales. While it may bother others, I feel the inclusion of more humor is great. It's the funniest film Spielberg's ever done. I love the way they explore medieval themes this time around and how it plays into the father-son relationship. Bringing Sallah and Marcus Brody back is great as well and adds to the epic boy's adventure of the third act. Dr. Elsa Schnieder's a fun femme fetale with some good comedic and dramatic moments. The action sequences from the opening River Phoenix prologue, the boat chase through Venice, motorcycle ride, tank battle and trials to reach the Grail are all epic.
I like Temple of Doom, but its major flaws relegate it to third place for me.
I find the movie poorly paced (after the life raft escape, the film slows down with exposition and slapstick humor. The main villains don't appear until an hour into the film), the search for the central artifact doesn't have the resonance of the first and third (Indy stumbles into the temple by accident and all he needs to do is snatch the stones from an altar. They don't have the Thuggees even get all five stones, so the battle never has a sense of urgency) and Willie Scott really is nails on a chalkboard. Yes, I respect they wanted a different love interest from Marion, but Willie's constant screaming and complaining is brutal. She does change a bit by the end, but her annoying aspects mostly remain.
The film still has its good bits: Harrison Ford does a good job, I enjoy Short Round (while I understand why he can be annoying to others, I give him a pass since he has some nice surrogate father-son bits with Indy and helps save the day), the darker aspects of the third act, and the great action sequences from Club Obi-Wan, the spiked room collapsing, the conveyor belt fight, the mine cars and the rope bridge finale remain fun. An entertaining adventure film to be sure, but thinner in plot and characterization compared to films 1 & 3.
While I would rate it as the least of the films, I think Kingdom of the Crystal Skull is a decent enough film and not the disaster its often made to be. It suffers from some goofy bits (the prairie dogs, the monkeys during the jungle chase), too many characters in the last act (Last Crusade did a much better job balancing out the sidekicks and villains while keeping Indy center stage) and the finale just doesn't have the sense of excitement the finales of the first three films had.
However, I feel Ford does a great job returning to the role and it's nice to see him reunite with Karen Allen. I like the entire first half from Area 51 to the investigation of the tomb in South America. It's a flawed film, but in my opinion, far from being the worst sequel to a great franchise (see: Godfather 3, the last Die Hard film, recent Terminator sequels and Alien prequels for worse).
"There is still hope." - Arwen, LotR "No man controls my destiny. Especially not one who attacks downwind and stinks of garlic." - Azim, ROBIN HOOD "Do you stop believing in the moon just because the sun comes out?" - Jack Frost, RISE OF THE GUARDIANS "I am no man." - Eowyn, LotR "I am Diana of Themyscira, daughter of Hippolyta, & your wrath upon this world is over." - Diana, WONDER WOMAN