SSB64: This Link is the Hero of Time from Ocarina of Time. The only other adult Link at the time of the game's release was the one from Zelda II, and that Link doesn't have the Hylian Shield or Boomerang that this Link wields.
Melee: It's plainly obvious that the four Zelda characters are all from Ocarina of Time: Link has the Hylian Shield, Young Link has the Kokiri Sword, Zelda can transform into Sheik, and Ganondorf has no other game to be from (at the time).
Brawl: This is where it gets a bit funny. Link here has pretty much an identical design as the Hero of Twilight (Twilight Princess), but with a hair colour much more like the OoT Link, and a fairy following him for a taunt and at the start of the Subspace Emissary (which TP Link doesn't usually have). Zelda also uses her design from Twilight Princess but can still turn into Sheik, who is purely an OoT character. So while they're mostly based on their Twilight Princess incarnations, they have a bit of OoT to them as well. Toon Link is obviously from The Wind Waker, and Ganondorf is as he appears in Twilight Princess.
SSB4: From what we know right now, Link is again some sort of conglomeration - he still has Twilight Princess bombs and is left-handed, and his model is overall mostly unchanged from Brawl, but his colour scheme is more Skyward Sword-like. Toon Link appears to once again be unambiguously from The Wind Waker, retaining the Wind Waker, Master Sword, and Hero's Shield. We don't yet know anything about other Zelda-series characters.