Most of the characters underneath the Link-Zelda-Ganondorf thing are from Wind Waker. The whale, the dragon, the dude with the fiddle, the bird chick, leaf-face... you've also got Majora's fairies and Skyward's Fi. Below that, it's a solid block of Twilight Princess. You've got the bar folks who help Link in various areas, the sage dude who looks after the kids, and what's-her-name with Epona. Below Ingo and Talon you've got the pirates from Wind Waker, as well as Link's sister and grandmother. Further down still is a lot of Majora's Mask stuff - the zora with the guitar, the elderly goron (I think), etc.
I don't recognize the old guys further below, but the middle one is - spoiler alert - Midna from Twilight Princess, with the Majora's Mask peddler beneath her. Wind Waker's boat is beside claw guy.
Then we've got a giant Gohma-ish eye, Zant from Twilight Princess, some dudes I don't recognize, and an assload of Majora's Mask. Then it's Ocarina's Ganon, Fierce Deity Link, a generic enemy, something that looks like Twilight Princess' Zelda but might not be, and the wolf that taught you new abilities in Twilight Princess. Not sure what's up with the baby in white.
EDIT: And there are some characters with the same appearance in multiple incarnations, so it's hard to pin down, like the Great Fairy and Tingle.