Belloq: Best villain in the Indy series. He always has a superior, "I'm better than you and you know it" attitude, is incredibly selfish, and believes he'll always win. It really portrays him as the anti-Indy. This is because Indy has trouble admitting when he's wrong and what he's doing is wrong, mainly due to his excellent track record.
Mola Ram is a living, breathing stereotype of everything that Americans fear when they go to a third-world country... taken back to the 1930s.
Donovan and Elsa: Easily the most dangerous villains when it comes to subtlety. They put on a facade that they're nice, ordinary, intelligent people, when really, they're cold-blooded monsters. When I read the novelization of The Last Crusade, I was shocked when I found out they betrayed them. It wasn't until later when I realized it made perfect sense, due to what happened prior to them revealing their true colors. I.e., Elsa ranscaking Donovan's apartment to look for the Grail diary, Donovan kidnapping Indy with shadowy characters.
Dovchenko and Irina: I personally found Irina and Dovchenko the most menacing villains in the Indy cast for personal reasons. My family on my mother's side were from present day Ukraine and Russia. Some of my relatives have lived in the Soviet Union during the darkest days of the Cold War. That being said, Irina is the classic case of a woman who wanted to pursue Stalin's dream, a man more deadly than Hitler. She wanted to take over the world, brainwash all of its inhabitants, and seek the ultimate form of knowledge. That is insanity at its worst. The wonderfully ironic ending was that she got exactly what she wished for... with a catch.
Anyone else think that Elsa Schneider and Irina Spalkov would make a deadly duo? They're both similar when it comes to goals and interests.