After reading some other opinions here, my first opinion is just re-inforced. Belloq is (in my opinion) by far the best Indy villain. If for no other reason than the fact that he was a fully developed character with realistic motivations. Donovan is a close second, but there is no history between him and Indy. That's one thing that makes Belloq such a great villain, you can tell from his interaction with Indy that their paths have crssede many times in the past. It almost comes across like a 'Batman/Joker' or 'Superman/Lex Luthor' type relationship. Plus it never came across as forced. That was a big problem with Wu-Han and Shorty. Those two were supposed to have had long relationships with Indy, but the chemistry never came across.
Donavan was decent, because his motivation was also something that came across as somewhat realistic. I mean the quest for eternal youth is a staple in story telling. He just didn't have the edge that Belloq's relationship with Indy had. It wasn't possible though, or Donavan would have seemed like Bellq II.
Mola Ram was the lamest Indy villain (again, just my opinion.) He was shallow and poorly written. There was just no depth there. His motivation was presumably world domination, but he just came across like a B movie bad guy (which WAS the inspiration for Indy movies, I'll admit.) Unlike the other two, he wasn't fleshed out to fit a feature length format. He retained the 1 dimensionality of a 15 minute serial villain.