It depends. I kind of have two signature Pokemon.
The first one is obviously my Plusle. That little electric rat has always been my good luck charm. In Colosseum when I was unable to defeat Ein, it was my Plusle who won. When I was going through the gyms in Hoenn, it was my underleveled Plusle that won my badges. It was my Plusle in Heartgold that kept singlehandedly took out the elite four and the champion at a measly level 80. Plusle will always be my favorite Pokemon, no matter what. The species as a whole has been reliable, scrappy, and the cutest Pokemon to date.
The second one is a bit more complicated. You see, I've never really cared about Typhlosion. I find the species to be somewhat boring. In my eyes, it's just another generic Fire type. However, I absolutely adore my Typhlosion. When the Pokemon fad ended, I was too afraid to buy the gen 2 games because I was afraid of being made fun of since I was still a young kid at the time. So I spent a couple years just replaying Blue version over, and over, and over again. Finally, it got stolen so I couldn't play at all after that. One day, I was at the video store, and I was going to rent a game. While there, my eye caught to Pokemon Colosseum. I nonchalantly grabbed it and put it in our cart, and we took it home. That night, I popped that thing right into my gamecube, and suddenly, my love had returned.
I failed at catching the shadow Makuhita because I didn't know the Pokeballs were kept in a different pocket. However, I did manage to snag a Quilava, and it became my partner. I always used it, even though it couldn't level up. I would switch the others out, but Quilava always stayed firmly in the first spot. When I finally got it to the point of purification, it grew a ton and became a powerhouse. I named it Burney, and when I beat the game, I traded it over to my Emerald version about 2 years later. It was the first Pokemon I got to level 100, and it's still helping me on my Black team to this very day.
Plusle and Typhlosion were my dream team as a kid. It is what brought me back to the franchise, and reminded me of my love for this series, and why I shouldn't be afraid to be passionate about something so great. I've had a lot of Pokemon that I've loved, but I will never love any Pokemon as much as these two.