Totodile is my favorite. It is very strong as Feraligatr and I love reptiles. Totodile had a specific charm that I couldn't find with the other starters in GSC, although I didn't dislike the others.
Charmander comes in close behind. It's one of the very first, and who wouldn't love to have a fire-breathing dragon? I'm really into the reptilian and "cool" Pokemon, and Charmander fits the bill well for me. I almost always started with one in Red and Blue.
Cyndaquil and Mudkipzzz I'm not overly fond of, but they're still cool beans. Typhlosion is AWESOME, and Swampert is strong and its electric-canceling Ground/Water type is convieniently unique! Chikorita is one I don't really like, but Bayleef is cool and I love Meganium. As a whole, I prefer the fire and water starters to the grass.
The only generation where I didn't really like the starters was DPP. I chose Piplup because I like penguins, and when I checked the starter chains, Empoleon looked the coolest. Infernape is probably really cool and powerful, but I just prefer Empoleon. And Turtwig is a Bulbasaur impostor from Hawaii. :p