Let's analyze a few weaknesses of his in some games.
Link to the Past: His human alterego, Aghanim, has hit attacks reflected right back at him with a simple bug net. Hitting him with the Master Sword hurts Link, but smacking an energy ball with a bug net sends it right back at him? Dang, that's some crazy material there.
Ocarina of Time: After robbing the kingdom of Hyrule of all bug nets, Ganondorf and his phantom self challenge the Hero of Time, using familiar attacks. Crafty Link, however, has learned how to take a common glass bottle and smack stuff with it, reflecting the same energy balls back at him. To Ganondorf's credit, he did actually learn how to hit it back with his cape. But when you get beaten by a piece of glass, it's hard to not laugh at how much you fail.
Wind Waker: Ganondorf has spent a lot of time in the sacred realm, becoming almost as competent as he has become fat. Apparently, he took combat instructions from Yoda, and now duel wields 2 badass swords. His phantom self, however, has learned absolutely nothing, being able to be defeated with the same bottles, by using the same attacks. You'd think he'd have given up on Dead Man's volley a century ago.
Twilight Princess: Due to the split timeline, the competence that Dorfy-boy has gained in the sacred realm is lost, and his body fat is added to his hair instead. Ganondorf sinks to a new low here. Rather than using his tried and true energy blasts, he decides to abandon all projectile attacks in favor of sword fighting. But what's this? Link has grabbed his pole and is flinging it around Ganondorf's faced. Pathetically, Ganondorf is so mystified by Link's massive pole that he can actually stand around for HOURS staring at it flowing in the wind, while Link just stab stab stabs him to death. You really really deserved that one, you dirty man.
Skyward Sword: To avoid spoilers, the boss is not actually Ganondorf, but could still be applied to him considering the relationship. It's a climactic battle, Link is approaching him, as lighting strikes randomly around the field. And then, he holds up.... A BUG NET!!! DUN DUN DUUUUUUN! What's amusing about this is not only does the boss stop attacking, but he actually WALKS SLOWLY AWAY FROM LINK!!! The sword of evil's bane doesn't scare you, but an oversized insect catcher does? "Great King of Evil" my ass!
Ganondorf has his cool points in the series, but when you're greatest weakness is something so pathetic like a piece of glass or a bug torturing device, then you've got some serious issues.
(I voted for Link/Ganon. Still pretty epic)
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You just lost the Game!