My top three would definitely be Articuno, Mewtwo, and Mew in that order.
I fell in love with Articuno because I thought it was gorgeous, and it was fun to Ice Beam the dragons. With Mewtwo, I definitely always found the lore interesting. I can remember reading the diary entries in the Pokémon Mansion, and then seeing Mewtwo's creation at the beginning of the first movie and just loving it. It's tough to pick between the two, but I have to go with Mew as my absolute favorite. The little guy was quite the enigma back in the day, and still is, I suppose. It was nearly impossible to get before the Mew Glitch, and wasn't even that widely known about for a while. Plus Mew is just so darn cute!