For the current metagame, I would argue that Gyarados is now the defining pokemon. It is the reason that every team has multiple electric attacks, and now without Mence, it is the primary target of Stealth Rock. Its new role as the most feared set up sweeper is the reason why HP electric has gone from 44% to 51% on Suicune in just two months. It is a near perfect counter to the two most used pokemon in the metagame, and is a real threat in its own right with arguably the best set up move, a great STAB, awesome attack, and surprising bulk.
As for the metagame throughout history, I would have to say Blissey. It is the reason why fighting is considered a good attacking type. Also, most physical attackers can overcome their respective walls by having the right attack (ice punch for Gliscor, Crunch for Rotom-A, etc.), while special attackers must resort to Explosion (a physical attack) or more indirect means (like Sub/Pain Split) to take down Blissey. Modest Adaptability Porygon-z needs Nasty Plot, Stealth Rock, and at least two layers of Spikes to guarantee an OHKO with the near suicidal Hyper Beam, and Heatran needs Specs, Flash Fire, Sun, Overheat, and Stealth Rock to OHKO the standard Blissey. Blissey is also the primary target of otherwise borderline tactics like Banded Pursuits or TrickScarves (outside the lead position).