Apparently nearly every Amiibo (excluding Pokemon)
It's like Game Freak doesn't want Pokemon to be Nintendo.
I think the real culprit is The Pokemon Company. From what I understand they are actually a real pain to work with, and they only want Pokemon to appear in games that they are the stars of. If Smash had been made a few years later there might not even be any Pokemon characters at all!
That would explain why there's no Pokémon content in Mario Kart or StreetPass Plaza. Does seem like Game Freak are pulling away from Nintendo a little too though, with their next game being published by Sega and released on every platform except Wii U.
The list seems pretty good, (apart from the missing Squid like Kirbychu mentioned) it's pretty much this:
Pokemon - All unlock generic "a" Amiibo logo Yoshi Splatoon - All unlock individual pattern. Link/Toon Link - unlock the same pattern. (WHY?) Yoshi (not woolly) - unlocks a non woolly Yoshi. Other Smash characters - unlock individual patterns for each character. Toad - Yep, you get Toad.
At least one thing that has to be praised about YWW Amiibo implementation, at least they went the extra mile and confirmed from the start that it seems to work with nearly everyone of them (unlike Mario Kart 8).