Consumerist has a great list of restaurant policies for ordering not-on-menu items. I used to get tacos supremes with beans instead of meat at Taco Bell, but haven’t done that for a while.
Chipotle nachos sound pretty good. Fresh stuff, great guacamole:
The Really Big Guide To Secret Menu Items – Consumerist
Chipotle: Chipotle will, like Taco Bell, make anything they have the ingredients for. Unlike Taco Bell, this is an official policy. Some suggestions: Nachos, Quesadilla, Individual Tacos, Taco Salads, Tiny Bean Burritos Using Taco Shells, Fresh Cilantro on Your Tacos, whatever you can think of.
Mark Eibner turned me on to making a custom taco salad at Chipotle. He goes for for the beans, chicken, cheese, lettuce, a little bit of each salsa, avoids rice. Awesome stuff, but kinda tough to eat with a plastic fork.
I wouldn’t want to be in line behind someone who really pushes the custom ordering envelope. Just because a restaurant will do it, fulfill your request.