Thrawn was definitely my favorite. What a great villain. Brilliant mind, an ambiguous mix of ruthlessness and honor. Although I generally sympathize with the Rebellion/New Republic (in other words: the good guys), Thrawn just captivated my interest, enough that I was almost hoping for him to win.
My second favorite would probably be Pellaeon, closely followed by Karrde. Pellaeon is really one of the few individual Imperials I've come to like. He was such a competent officer in the trilogy who didn't seem as arrogant as lots of other individual Imperials and he also seemed to care about his crew. Being a supporter of the Empire and also showing a bit xenophobia now and then, he's not exactly an outstanding rolemodel but he seems to be an Imperial with more morals then many others. He just seems like a grandpa figure, lol. Especially in the Hands of Thrawn-duology where he's even more liekable.
Karrde is a fascinating character as well. An astute smuggler who knows how to play the cards he's dealt with.
Number four would probably be Aves, number five Mara, and finally Ghent. However, I liked all of them when reading the trilogy.
^I agree. Garm Bel Iblis is a great character as well