Okay, let's try naming them all.

From the Top:

The Three Goddesses, Farore, Nayru and Din

The Six Sages: Rauru (with Kaepora Gaebora), Impa, Saria, Nabooru, Ruto and Darunia. In the middle of them seems to be the King of Hyrule, Daphnes Nohansen Hyrule.

The Three Triforce Holders: Link, Zelda and Gannondorf

A bunch of Great Fairies in their various incarnations, including the Queen of the Fairies and the Fairy posessing the Great Fairy's Sword.

The Wind Fish, on the left

The Three Holders of the Pearls: Valoo on the right, Jabun below him, and the young Great Deku Tree (pictured next to the old Great Deku Tree)

The Sages of Wind: Makar and Fado

The Sages of Earth: Medli and Laruto

Now for the huge mass of characters:

In the top left is Renado, shaman of Kakariko Village. Next to him is the group that helps Link in TP: Auru, Ashei, Rusl and Shad (I had to look the names up, sorry I couldn't do it from memory). To the right of them is Marin and Tarin. Next is Ilia and Epona. Below and to the right of Epona is Talon and Ingo.

Starting from the left again, we have Anju and Kafei, followed by Linebeck. Below him and to the right is Aryll, followed by Tetra's pirate crew (don't ask me to name all of them) and Link's Grandmother. Below Anju and Kafei is Tingle (\shudder**). Below Linebeck is Cremia and Romani.

Again, starting from the left we have the Indigo-Go's: Tijo, Lulu, Evan, Mikau and Japas from top to bottom (had to look up those names too). Then we see a Skull Kid and Mido. Above and to the right of them are Ralph and Maple. On the far right is Darmani (or possibly his ghost). Below Darmani is the Goron elder from MM and his son. Below the Skull Kid and Mido we see MM's Deku King, Deku Princess and Deku Butler.

The next row contains the King of Red Lions, Byrne, Anjean, Midna in Twili form with the Happy Mask Salesman below her, Oshus, Ezlo in Minish form (not 100% sure) and Ezlo in Cap form.

I'm not sure who the giant eyeball belongs to. It might be Vaati transformed, a Nightmare from LA, or Gohma in one of her incarnations.

From right to left we have Veran, Zant, Agahnim, Vaati in human form and Onox. Below is Koume, the Moon from MM, Kotake and Chancellor Cole.

Below them we see the children inside the Moon from MM: one wearing Majora's Mask and the other four wearing the boss masks. On the sides are the four giants.

Below this is Ganon in Beast Form. To his left is the fierce Deity and to the right is Dark Link.

I believe the knightly figure in the center is the Hero's Spirit from TP and the wolf to the right of him is the Golden Wolf.

To the left of the Hero's Spirit is a woman in a cloak holding a baby. Though the cloak is similar to the one Zelda wore in TP, this is most likely Link's mother holding Baby Link before giving him to the Great Deku Tree (pre-OoT).

Phew!

I think I did alright. Hopefully this will get noticed.