Here is a list of GOOD characters to counter with
Megaman (if your lemon game is playiing the matchup correctly, you can turn off Links tools)
Fox (just rush down and shine the boomerang on the returning hitbox, and you win)
Falcon (just like fox, he's fast, so Link gets bodied the moment he gets in)
Zero Suit Samus (Like Fox and Falcon, but with more tools, and a 0 to death combo on Link at the ledge)
Pichu/Pikachu (again, the speed is an issue for Link, except these rats can actually edge guard him safely unlike most the cast)
Palutina (just use your orbs whenever you see Link telegraph an item attack, and it will 100% of the time stuff out the item + counter for edge guard)
Here is a list of soft counters
Villager / Isabel (Just pocket their bomb and spam retreating Fair and Bair pressure, you can't really lose because your aerials stuff out his items)
Zelda (throw out Phantom whenever they throw out a boomerang because phantom will block it and then sit in place to block more, plus neutral special)
Roy/Lucina/Marth/Chrom (Can easily outspeed and outspace, if you are good at evading items, and easy edge guards with counter)
Sonic (rush down and grab, then go for EZ up special gimps with your spring)
Honorable Mention
SNAKE
Yes, I said it, Snake is a VALUABLE counter pick. I saved him for last because snakes claim that he's bad against Link, but he's not. The same argument they use to make such a statement is the same argument that can be used against them, that being, Link and Snake stop eachothers projectiles with eachothers projectiles. While this does prevent Link from advancing, it doesn't stop Snake from doing Snake. You see, even if the Link stops your grenade with a boomerang or bomb.... it's still sitting in center stage and controlling space. That Link wont approach unless they are crazy or just bad at the game. Blocking projectiles with grenade only to have that grenade sit in neutral and protect you isn't AT ALL a bad thing for Snake, because now he can setup Snake traps or Nikita, etc. Another thing that Snakes REFUSE to acknowledge is that Links ONLY true strength is his ability to kill people off stage with a widespread tool kit designed to do so.... the only problem is.... it wont do anything against Snake while he's recovering. The only thing a Link has to edge guard Snake is down air which is not only situational in snakes recovery path, but also risky because if you miss, you might be dead. So all in all, Snake can shut down Links items with a better projectile (which also breaks combos), and turns off Links one in game advantage, his ability to edge guard.
I recommend Snake or the first list.
Jigglypuff can get around projectiles pretty well.
Since the down of Smash Melee, one of Jigglypuffs worst matchups is Link/YoungLink because being in the air as a floaty while having mobility cut off by items and being left to almost always lethal disjointed hitbox just doesn't fair too well for the ball of puff. I dpn't recommend puff for the same reason I don't recommend Peach.
I agree with the Fox, the Metaknight is stage dependent and by my experience both playing with Diddy and with Link, both against eachother also, Link has quite a few advantages in the Ditty matchup.