Ho boy! I'm in the process of making a team of my favourites. I guess they'd go like this...
Murkrow: Like KINGBeerZ said, its design is awesome and I've always preferred using it instead of Honchkrow. Love that it got Prankster!
Golduck: I thought its design was cool from the moment I saw it, but when I first saw that episode where a Golduck shows up and Misty believes it's her Psyduck, I was in loooooove! It just looked so cool, and I haven't used one since Platinum. I'm amending that right now!
Ledian: Oh how I wish, how I wish that Ledian was viable in competitive play because its design is so freakin' cool! Power Ranger shenanigans going on! It works pretty well on my team as an annoyance, but I wish it could do more. Maybe next generation, Game Freak will give its Attack stat a boost, so's Iron Fist would be useful. Aaah well.
Furret: Arrr! Adorable! My first Gold team had one, and I loved kicking butt all the way with it to Mt. Silver! Haven't figured out a niche for it in my team though. Hmm...
Nidorino: Makes sense right? I mean, that's the first Pokemon you see in Red/Blue. The second I saw it, it was my favourite Pokemon of the original games. Its stats aren't great so I can't really use one online, so I'm going with Nidoking instead.
And my favourite Pokemon ever!
Arrgg! I love him so much, I've made sure to have one in every single Pokemon game since Gold. I don't remember much about my original Gold team, but I do remember him, and how I accidentally taught him Flash at the very end before facing Red, overriding Thunderpunch. I was pretty upset. I'm not too fond of his Mega Evolution (I guess it's the ears/horns), but my love for this guy is unending!