Hi - DS chooses our resort based on whether the food court has Mickey waffles! Only listing the info we learned last week because it changed even since a few months ago at certain resorts:
As of mid-February 2015:
NO Mickey waffles: Pop Century; Art of Animation. (Both Pop and AoA have resort-specific themed waffles (which I think is so cool); all are small size now (the large Pop waffle is gone as of 1/2015; adult portion gets an extra waffle.) Pop will put whipped cream on your waffles (because the waffle area shares with the ice cream area).
HAVE Mickey waffles: All Star Movies CS; The Contempo Cafe (CS at CR); The Wave (non-character TS at CR); Chef Mickeys, Tusker House, Hollywood & Vine.
I can't believe I don't remember, but I do have a dim memory that Contempo had not only the small sized Mickey waffles for kid meal, but also the large ones for adult breakfast. But don't rely on me for that. Aforementioned character meals and The Wave only have the small sized ones. Not sure if ASMo has large (they do have small).
We stayed at POR, POFQ 1.5 and 2 years ago, and they both had mickey waffles back then. Hoping someone else can let us know - I want to stay at POR in April, but DS wants ASMo (for certainty of Mickey waffles!).
PS I know the price is high ($41 plus tip for an adult), but if you love the small Mickey waffles you might have to get to Chef Mickey's. They make them right in front of you (take the ones in back): they are crisp, hot and amazing. Food courts take so long to get from where you stand in line to order, through the line to pay, to sitting down, they are just lose the crisp edges by then. That said, I bet The Wave would make them fresh for you if you mentioned you're an aficionado (their buffet is $21 adult, and includes sweet potato pancakes - and is SO much quieter than Chef Mickey's).
I can't believe I have this much info about waffles at WDW!