RED (for the obvious reasons)
Nate (looks abit like Tai from Digimon, the first anime character I really liked)
Ethan (he looks so cool)
Leaf (just amazing and I really like Blue from the Manga)
Sapphire (awesome in the Manga compared to May, who I found to be abit whiny and annoying in the Anime)
Iris (League Champion, need I say more)
To me, the true stars of the pokemon franchise, are and always will be, the pokemon themselves.
I sometimes wonder why the protagonists get such fan followings, they don't really have personalities of their own, as they are supposed to represent the player as I already mentioned. If anything I would like to customize my own protagonist. Maybe in gen 6 I will get my wish..
Those sentiments are specific to the games but the OP said "in Pokemon" which would extend to other media such as the Manga and the Anime where, for the most part, those game avatars are given personalities and take on a life of their own.