Lugia...it was such a recognizable Pokemon back when I was a child and it always seemed rather "cool" to me in terms of design. I'm also quite fond of Celebi and Suicune.
The Regi Trio. I like how you had to solve the briaire (or whatever it is spelled) puzzle to catch them. Also, the battle theme perfectly suited the feeling of having a huge giant Pokemon that you had to catch. I also loved their cries as well. (Especially Regice's 'Hello')