Most useless central character: Tough call. Most central characters are pretty badass in their own way and serve as the focal point of a team. Tidus never really got to leadership position, but he did serve to motivate the team at times, and was definitely a great swordsman and supports Auron and Yuna nicely with hastega. I'd have to go with the main character in Diablo one. All that lovely warm lava around to dunk the soul-stone in, and you stab yourself in the head with it instead, getting possessed by the devil by a different name? I went through sixteen floors of hell for this?!!! Throw the cursed stone into the sea already!
Most useless (well, counter-productive) main character: Knuckles. He cripples his own side as often as he harms the enemy, regularly has to shatter his own emerald (aside from frequently being asleep at the helm and letting it get stolen) and just generally pisses off or gets in the way of the rest of his allies, usually to the great benifit of his enemies. He also never does anything to intentionally support the rest of the cast (except briefly in SA2's cannon core.) Such a powerful character, such a tiny brain.
Well, ok, I have to admit, he did kinda save the day with the master emerald near the end of SA2... but only after Rouge had to remind him that the master emeralds main purpose was to nullify the chaos emeralds! He's supposed to be the authority on the darn thing! Maybe Sonic should just guard all the emeralds...
Most useless supporting character: I'd have to go with Quark from Ratchet and Clank. Its just as well Ratchet is hyper-competent. The fact that he steals all of Ratchets credit doesn't help either.
Most useless NPC: All shopkeepers when there is an emergency in the universe. A group of heroes are trying to save the world and you charge them money? Also, the fan from Mass Effect 1. If you like Shepard so much and want to help him/her, join the *gratuitous swearing* military!
Most ineffectual villain: I'm tempted to say Eggman, but he seems to have taken a level in badass lately. I'd say Ganondorf. He regularly loses to a teenager (or sometimes a nine-year old boy) who has had no sword training and is possessed not with super-powers like most heroes, but just with apparently suicidal courage. When you have the magical ability to resurrect dragons and still lose to a nine year old in a sixteen year olds body who comes from the local flower-child society, you know you've missed a few crucial points on the evil overlords list!
Which is why I have to nominate Link for the most scarily competent hero ever. Say what you like about the awesome badass heroes with the BFG's, BFS's and lightning fire from their arses, I'm impressed by the dude who can take down just as scary a big bad before he's turned ten!... with a short sword and bow! What would he have been like if he'd been raised as a fully-trained knight in Hyrule?