Many on the list have had a big effect on the metagame, but many of them are cyclical. Scizor took out the fast and frail with Bullet Punch, threatened the stalwart with a stab U-Turn and punished the fleeing with Pursuit. In comes the pokemon that can deal with this, like Heatran and so on.
The only one I can think of that wasn't based on a cycle but you always had to watch out for was Tyranitar. Various T-Tar sets worked in cycles, of course, but the pokemon itself didn't fluctuate a great deal, he was always there. This makes sense. Tyranitar is one of the psudo's graced with great stats and movepool. 4th gen gave him many new toys and yet with all of this he is held back by common weaknesses including a 4x weakness to fighting. Why then do I choose Tyranitar? Because I don't choose him only for what he can do, but for what his ability has done.
If you take a look at many of the war stories in the archive you'll see this message many times "Sandstorm damage has been omitted". SS's 6% has been so ingrained into all of us that it is automatically calculated in our thoughts. In addition, SS boosts the special def of its main set up and, most importantly, it has acted as a bouncer keeping the other weather effects from being the problem that they are in the lower tiers. Want to use rain? It has been a raging debate down in UU about being banworthy. In OU, however- watch out for T-Tar. He'll mess up your plan quickly.
But this was, for the most part, present in Gen 3. Why then does this make T-Tar the pokemon with the most effect on the metagame? I say it is because of synergy, or how well it all works with everything else that changed in the metagame. T-Tar as a pokemon checks many threats and is a powerhouse on his own right. An automatic sandstorm limits otherwise viable strategies, and damages each turn. Add this to the varying damage of stealth rock & the added power attacks on Gen4 and everything comes together go smoothly. T-Tar has had the most effect on Gen.4 because you don't notice how much it affects you when you're building a team or planning a strategy, it had become second nature.
IMO, anyway. Obviously other things have had a great impact at one time or another but T-Tar has gradually built up a sand castle empire, and occasionally drops by to shake stuff up.