Bisharp
Manaphy
Mega Mawile
In no particular order
1) Bisharp is because it forms half of the DeoSharp core (seriously, this archtype thing is one of the most dumb things ever). While Deoxys is more crucial to these teams, Bisharp's period in the metagame is far longer and it still is one of the most terrifying sweepers in OU.
2) Manaphy, as I mentioned in the nomination, makes Stall and Balance teams almost unviable because of how easily it takes advantage of the passive mons in these teams. Until now, it is still slapped into teams to break through the fat teams that are thriving in the meta.
3) It also had the tools to do whatever it wants; STAB, Sucker Punch, Fire Fang, Focus Punch, Substitute; making switching into it nigh impossible and alongside Aegislash, made most Psychic-types obsolete in the metagame. This is also the Pokemon that almost gave Arcanine a niche in the metagame.