Which Zelda and Link are featured in the Super Smash Bros. series?
In the original Super Smash Bros. and Melee it's the Link from Ocarina of Time. In Brawl, they changed it to the Twilight Princess Link.
I figured this out by comparing the pictures of the Link from the Zelda games with his pictures from the SSB games. Ocarina of Time was only game out with that shield design when SSB64 and Melee came out. Twilight Princess has the same shield design, but Link's appearance in Brawl is basically identical to his in Twilight Princess. Also, that's what the Zelda Wikia says. :P
Zelda is also from Ocarina of Time in Melee and Twilight Princess in Brawl, since she also matches those looks.
Sheik is from Ocarina of Time in Melee, obviously since that the only game she's been in, however it is said that her Brawl appearance is based on conceptual designs for her in Twilight Princess.
It's claimed Ganondorf's Melee appearance is based of the SpaceWorld demo, although he looks a lot like he did in Ocarina of Time as well, and his Brawl appearance is again from Twilight Princess.
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.