Hmm.. Impossible to decide, so I'm just going to throw out one of my favorites that is less likely to have been chosen by other people.
Valoo. He only shows up in one game, and only a couple of times in that game, but he's a dragon. A non-evil one, at that. Named a Charmander in my fan fiction after him.
Oh, and I loved Mia, the named Remlit in Skyward Sword. She's adorable, and reminds me very much of my own pet cat(who coincidentally looks like a Remlit, has an unpredictible temperment, and is named Mia)