The Judge will always be a favourite of mine, he's just so... Out there. You do get the feeling he hasn't got a clue what's going on, but sometimes he has these incredibly badass moments, like forcing Von Karma to submit himself to the metal detector. Speaking of Von Karma...
Manfred is the most magnificent of the magnificent bastards in the series, despite the bloody finger snapping, and the demonic OBJECTIONS. His plan to frame Edgeworth for Hammond's murder, and for his own father's was pretty damn awesome. Plus, I like having to adjust my strategies on the fly, which you had to do when facing him.
Finally, Ambassador Colias Palaeno, simply because he is the least obstructive, most helpful character in any Ace Attorney game, ever. He looks incredibly suspicious with his overly-large smile, and constant hand-rubbing, but does literally all he can to aid Edgeworth's investigation, including stopping Alba from leaving.
Honorable mention: Lamiroir, if only for her GORGEOUS theme... By the same token, Detective Badd.