Every RPG has that big bad guy but how many of them over the years have been not as good as a secondary villain in the story. For every Kefka from Final Fantasy VI that was able to dominate the screen, there are just as many villains that couldn't hold a candle to the secondary villain. These are villains that weren't the main attraction but ended up stealing the show.
Team Rocket (Pokemon)
This is a weird one. Team Rocket the evil syndicate is actually not the main villain of the first two series of Pokemon titles. It's the rivals Blue and Silver that are actually your main adversaries. So why is Team Rocket memorable? The anime helps but the reason has to do with the fact they have since been the only team that didn't look ridiculous and were actually evil. They dressed in dark clothing and looked like plain clothes soldiers compared to Team Magma's cat eared hoodies or Team Plasma's templar get up. These guys also were everywhere and had a really awesome boss ,Giovanni, who also was a gym leader. Compared to later syndicates in Pokemon, Team Rocket was up to no good and were proud of it. They had no interest in anything but power and corruption without relying on legendary Pokemon to do it.
Rufus Shinra (Final Fantasy VII)
The second head of Shinra makes his presence known immediately by attacking the party in Final Fantasy VII with a shotgun. Rufus is everything his father wasn't; that being threatening and vengeful. He spends the game hunting Sephiroth and casually attempts to execute two of your party members. At the game's climax he is blasted to hell by a large laser blast from one of the weapon monsters, and still lives. Other Final Fantasy VII tie ins have shown him to be the financial backer to the terrorist group AVALANCHE just to stick it to his father, the then head of Shinra.