I like this thread.
G1 (RGBY): Venusaur
Still #1 in my book. Originally my favourite was Vulpix, but that shifted when it looked far too wussy to have Vulpix as a favourite. My love for Venusaur stems from the mega badassery that my very first Pokemon featured. We all have a special place for our first Pokemon. Dragonite is #2, incidentally.
G2 (GSC): Quagsire
It was a toss up between Quagsire, Ampharos and Typhlosion. In the end I decided Quagsire, because I just remember being so excited by a water Pokemon that was resistant to electricity. Yeah I know, 4x grass weakness, but Quag, like nearly every other water Pokemon can counter with Ice Beam. Poor Grass Pokes are so screwed over by Ice Beam. I liked using Rollout with Quag, though I doubt I ever really used it well.
G3 (RSE): Swellow
Really close decision between Swellow and Breloom. In the end I went Swellow because this was the first Pokemon that I ever used tactically. Focus Band + Endeavour, with a little bit of Double Team thrown in to increase annoyance... I never intended to have a Swellow on my Ruby team, but it worked its way onto the roster by just being awesome at taking down enemies it really shouldn't. It got its ass kicked, and that made it just so much better.
G4 (DPP): Mismagius
Suicide Magus FTW. Mean Look + Perish Song? Great fun. It was the kamikaze rebirth of Trapbat, and I never grew tired of it. I should have named it Chiaotzu.
G5 (BW): Sawsbuck
It's still early days and I'm testing different Pogeys out, but so far Sawsbuck has been the most effective. Horn Leech+Leech Seed+Leftovers/Shell Bell = a whole lot of recovered HP. Add on Thunder Wave, and I intended to have Swagger in there to add to the opponent's annoyance, but Jump Kick just proved too effective to scrap, to the point where I actually use it more than Horn Leech. Anyhow, annoying Pokemon = good fun!