Well, here's my signature Pokemon...
Yellow-Nidoking.
I had extreme trouble defeating Brock with Pikachu and Pidgey, but I was young then, type advantages meant nothing to me. But then a friend told me that Nidoran learnt DoubleKick, and said it was really strong. It was the first time I had beaten a GymLeader, and from then I used nothing but Nidoran, who evolved into Nidorino, and then Nidoking.
Silver-Dragonite
My highest level Pokemon that I trained from birth. I won a Dratini at the GameCorner, then I bred it. Soon I was taking on the EliteFour with just my Dragonite. Ahh... Good times.
Ruby-Marshtomp
While I had many other Pokemon, Marshtomp was by far the most commonly used, however, this was closely matched with a Flygon on a later game, which I used almost as much.
Emerald-Nincada+Shedinja
I can't decide between the two, mainly because they were often used together in double battles. Shedinja prepared some support moves while Nincada swept in for the kill, a perfect combination.
FireRed-Nidoking+Nidoqueen
I had to for the nostalgia, but since the addition of DoubleBattles, I felt the need to add Nidokings counterpart to the team. Their pure power was unstopable, and their moves worked in perfect unison.
Diamond-Empoleon
Ah, Empoleon... I borrowed Diamond from a relative, so my time with Empoleon was short-lived, but in that time it smashed through the Gymleaders and had moves effective enough to compete in a contest.
Pearl-Torterra
At first I chose Piplup, in an attempt to repeat the previous Empoleons effectiveness. But it failed to measure up. So I restarted the game, and chose Turtwig. While it failed to live upto Empoleon on Diamond, he was one of the most reliable fighters I've seen in the Pokemon games.
Platinum-Rampardos/Bastardos
Throughout Diamond and Pearl, I tested both the ancient Pokemon. So I traded in both of them to Platinum and quickly became two of my favourite fighters. Nuf said.
SoulSilver-Sunflora
Don't ask why, but as soon as I saw the Sunkern at the park, I had to catch it. Unfortunatly, I failed to find a Sunstone, so it reached Lv.35 before evolving. Eventually I gave up looking and checked the internet, and soon evolved it into a Sunflora.
Sunnyday, Synthesis, Solarbeam, Chlorophil combo-Woot...
So currently, it's Sunflora (Still don't ask). I just hope they're available in Isshu!