I like the one in my signature (Charizard), but there's something highly amusing about eHalcyon's signature with the Cyndaquil mooning whoever looks at it.
Cyndaquil is just a little confused and facing the wrong way.
Also, the Bulbasaur and Piplup are shiny.
They aren't actually my favourite pokemon. Well, Cyndaquil and its line is one of my favourites for aesthetics. Bulbasaur is my favourite gen I starter and Piplup is my favourite gen IV starter, though it's close between all of them. Empoleon is awesome for its typing. Turtwig is adorable and Torterra is an amazing design -- he is a freaking continent.
Look at this. Chimchar and its line is cool too. My least favourite of the three, but still awesome.
I didn't actually play through gen III originally (I have a copy of Emerald now; still unfinished) and I actually don't much like any of the gen V starters.
It's hard for me to nail down my favourite overall pokemon though. Chandelure and Flygon are high up on my list. I love my paraflinch Togekiss in SoulSilver. I am a big fan of Ferrothorn just because I'd always thought that Grass/Steel would be a great typing (for gen VI, I am hoping for Ghost/Steel). I could go on.