"Who is the strongest?" is not even a measurement of who would in in a fight. Link can defeat Ganondorf, but I would say Ganondorf is more powerful.
Who is the best at their best? In order:
1, 2 & 3: Link, Zelda, Ganondorf, with the Triforce
4: Pokemon Trainer
5: Mewtwo
Who would win in a fight? Well, what kind of fight? Are they just dropped into a pitch-white, open room within 100m of each other, knowing who they will face? Mewtwo. Are they dropped in a post-apocalyptic world as the last ones alive? Samus. Is it a bar-fight? Captain Falcon.
It's all conditional.