I think that Sonic would be the strongest.
It's a well-known scientific fact that physical damage is caused by momentum. Momentum is expressed as the weight of a moving object, multiplied by it's velocity. A good example of this would be a bullet. Sonic, as everyone knows, is a source of nigh-infinite velocity. Q.E.D., a source of nigh-infinite momentum and a source of nigh-infinite physical damage. Also, he's capable of reacting to changes in landscape while moving in excess of the speed of sound. Therefore, his reaction time must be nearly instantaneous. Basically, everything must move like it's in slow motion for him. (No wonder he's so impatient.) It's like he's invincible. And has unlimited physical power. And he could bring that physical power to bear instantly. For example, get behind Marth and slash his neck with his quills before he can even get into a fighting stance.
You might think that an enemy covered in armor, like Bowser, would beat him. But any physical object must have some upper limit to the amount of physical damage, or stress, it can take, and Sonic has (from his perspective) an infinite amount of time to apply that stress.
So basically, Sonic could kill anyone without some sort of kinetic-energy-nullifier, and avoid any attack that moves slower than he does. Even if you tried to nuke him, he could be well on the other side of the planet in the time it takes to explode, and be back just as quickly. So basically, he's invincible to anything that doesn't completely destroy the planet he's standing on. (Apocalyptic Falcon Punch does not exist.)
There's a few other perks to moving infinitely quickly. For starters, things that vibrate at a certain frequency can pass through solid objects. He could walk into a landmaster and snap Fox's neck. Or walk into Fox and snap Fox's heart. And there's plenty besides that.
There would only be two reasonable ways to take him out: Sneak up on him, (Advantage Snake) which would require knowing where he is before the fight starts. And he's always moving. Easier said than done. Set a trap, perhaps?
The other way would be telekinesis. (Advantage Mewtwo, possibly Ness and Lucas. Never seen them do it, though.) That would be the kinetic-energy-nullifier I mentioned earlier. It's clear that he has problems with telekinetics (Remember Silver?). I suppose Sonic could avoid a psychic head-squisher by moving so fast that Mewtwo couldn't know where he was, but that'd be very situational.
As for Ganondorf...Well, Sonic's invincible to anything that moves slower than him, and Ganondorf's just plain invincible. I guess Ganondorf would eventually win that one, but Sonic would probably get bored and leave before either of them died. After making Ganondorf look like a humongous ***, of course.
