Toon Link is the most different Link. All the other forms of Link are fairly similar. He uses different weapons, lives in a post-Hyrule time/era, and moves, acts, fights, and even walks completely differently. His tilt attacks could be a little different, but his very motions with nearly every attack is completely different. (besides, Link always is a bottom feeder in smash, maybe Melee aside)
As for the Zelda timeline (without getting into everything), all you need to know is it takes place in Hyrule, minus all the Toon Link games, which happen after Ocarina of Time.
First game chronilogically:
Minish Cap
A Link to the Past then takes place.
Then somewhere after that, Ocarina of Time, and then Majora's Mask.
Twilight Princess takes place some time after that.
Then somewhere after that, the Wind Waker, then Phantom Hourglass, then Spirit Tracks.
The rest go wherever.