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I don't know about the waffle with eyes, but could it be Logical Journey of the Zoombinis or another game in that series? I played Mountain Rescue when I was young, and I remember there being a character creator.
Edited by DrNoPuma Very good kittyIt came out about a decade earlier than the time period you mentioned, but Awesome Animated Monster Maker was a PC game about making monsters out of different parts. There don't seem to be many videos around but I remember one part had monsters made out of food, and I think some of the pieces you could use for your monster were food as well.

I remember playing a game on a school computer during either first, second, or third grade (so some time between 2003 and 2006). It was an educational game where you were in some kind of alien/monster world and you got to make your own alien/monster character. I only remember that one of the things you could make was a waffle with eyes, or something. That's all I can remember.