My favorite Gym Leader of Kanto had to be Blue. He's the only Leader to use a team that isn't of a specific type, and even though he's no longer your rival, it's still satisfying to beat him in HG/SS.
I was going to pick Clair for my favorite Johto Gym Leader, but remembered that we had Drayden/Iris as Gym Leaders in B/W, so she no longer had a unique typing. I guess my favorite would be Jasmine, as she actually played a role in the game outside her Gym battle, and Steel is a tough type to face if unprepared.