Well, I guess you can say my main Pokemon in Kanto were Eevee and its evolutions, due to obvious reasons...
I never played any Johto games (how sad of me...), so next would be in Hoenn. Swellow all the way, mainly due to the fact it was, like, perfect for a sweeper, and had such great moves for any cool contest that it was just begging from me to use it. Plusle and Minun can also be considered trademark Pokemon here, due to the fact that they're the ones who made me interested in Pokemon again, and they're just awesome during 2-on-2 battles.
Sinnoh, I had quite a few. Luxray and Floatzie were my main ones, though I had a bunch of others. XD
Outside of the games, though? If people have been following my RP characters' main Pokemon team, almost everyone will always see either Ralts or Kirlia (and eventually Gardevoir if an RP went that far, or if I ever wrote a fic that made that Ralts/Kirlia evolve, which both have yet to happen). Also, once my team's a bit straightened up, Lanturn's also a main Pokemon seen often, as is Sandslash. But the Ralts family is always in with my characters. ^^
I really have no "trademark Pokemon" outside of Eevee and Ralts (I've always had a Ralts in my team if I could find one early on), though both are slightly common "favorite Pokemon" or trademark Pokemon. But meh. XD