Ho-oh is definitely one of my favourites. The first Pokemon game I ever played was Gold, so he'll always have a spot in my heart because of that, but additionally, he can revive the fucking dead. That is the most amazing, miraculous power ever.
Reshiram is another one. I really like his design, from his appearance to his typing, and I also like the fact that he espouses the idea of truth.
It's actually pretty hard to choose a third, but I guess I'll go with Mewtwo. In my head-canon, I view him as the most powerful Pokemon in the world (exception: Arceus), and the first Pokemon movie is the only one I ever really watched, so I definitely got some nostalgia from that.
Frankly, I find it easier picking non-legendaries. Tyranitar, Scizor and Haxorus FTW!