My favorite Pokémon is Entei; while he's pretty much nothing special in the Game Boy games - more like a Houndoom on steroids then anything else - I like his appearance and voice and roars. He just looks powerful, or at least to me, whereas Raikou and Suicune seem to be more focused on being built for speed and agility. All the different masks on his face give him an interesting appearance, and the smoke trailing down his back is just...just...cool. The four stiff wings on his sides are a nice touch, I believe. Adds to the what-exactly-am-I-looking-at/mythology-like feature.
Rukario is my other favorite. But mainly what made me like him was the 8th movie, not so much him himself, if that makes any sense. I did like his appearance (especially the second pair of ears, AKA the four black things on the back of his head), though, and the orientation of the wrist spikes was pretty different from the norm. Normally spikes on the wrists are pointing down, in my experience....