Raiders of the Lost Ark: My main issue with the movie? The whole plot is pointless. Dr. Jones never had to go through anything to get the Ark before the Nazis. The ending would have been pretty much the same, except instead of having a bunch of Nazis with hostages going to an island and only the hostages coming back, you'd have them go to the island... never to return. Sure, the Ark gets stored in the warehouse, but the only people who could ever use it without melting and exploding are Levites, soooo... what?
Temple of Doom: You have annoying sidekicks, a scene filled with bizarre 'food', a forgettable plot element (I keep forgetting magical stones and a grudge between two 'Hindu Gods' is involved) and just corny to the extreme. Frankly, if the villain hadn't torn that guy's heart out and burnt him alive in a lava pit, I do not think anyone would remember this movie.
The Last Crusade: Here only for sake of completeness. The movie is good, and if you vote it as the worst, you have no soul

The Kingdom of the Crystal Skull: Has a bunch of CGI which really separates its from the rest of the series, a lead-lined fridge, Shaila leBuff or whatever that annoying kid's name is, and perhaps the most jarring of all, aliens. No other science fiction elements exist anywhere else in the series, but here, out of nowhere, we have aliens.
So, which is the worst, and why?