Gen 1: Mewtwo.
Being the strongest Pokémon of them all, Mewtwo was a really awesome Psychic Type in the old days. Gen VI gave it TWO Mega Evolutions to take advantage of its' broad movepool, which really helps, in my opinion.
Gen 2: Houndoom
Dark Types are awesome, which is part of why I like Houndoom. It's based off the hellhound and a Doberman Pinscher. It even got a Mega Evolution and Solar Power, which is essentially a free Choice Specs in Sunlight. It's also one of those uncommon special-based Dark Type users. (Which are Dark Types with a respectable Sp. Atk stat, FYI.)
Gen 3: Rayquaza
Whenever I got into difficulty facing Juan and his Kingdra while playing Emerald, and with no useful Dragons or no existence of the Fairy Typing back then, I often had to catch a Rayquaza to defeat Juan, the Elite Four and Champion Wallace. It's got two high offensive Stats and a broad movepool to choose from. I'm hoping it gets a Primal Form to really jack up it's power.
Gen 4: Lucario
Playable character in Super Smash Bros. Brawl? Check!
Major character in Lucario & The Mystery of Mew? Check!
A rare Fighting Type with good Special Attack? Check!
Steel recently having the upper hand against Fairies? Check!
Epic Mega Evolution with the ever so handy Adaptability Ability? Check!
Did I mention the broad movepool? Check!
These reasons are why Lucario's one of the best Generation 4 Pokémon, in my opinion.
Gen 5: Volcarona
Bug Types were usually generic Pokémon with average stats, with some notable exceptions (Yanmega, Heracross, Shuckle, and Forretress) when it came to power and defence. However, the fifth Generation brought us some amazing evolved Bug Types, like Galvantula, Accelgor and Escavalier. Out of all those strong bugs, Volcarona really stood out, with Stats on par with a Legendary Pokémon and having access to the very handy Quiver Dance, Volcarona is a major threat in the competitive environment, even to this day. Bug/Fire is a special combo, since it does wreck some of the best major players in OU. (Like Scizor and Excadrill, for example.)
Gen 6: Greninja
Greninja would have been a fairly mediocre Starter evolution if it hadn't been for it's amazing Hidden Ability, Protean, which gives a lot of the moves it could learn gain STAB, and with it's stats on par with Sceptile, it really stands out on its' own. It even got to be a new playable fighter in the new Super Smash Bros. game. It's also a ninja, which are always awesome to see.