As someone who doesn't get to Ames often, I would prefer to go to Dublin Bay or Great Plains.
Ah, Ames food... how I miss ye among this wasteland of bad restaurants known as Dubuque.
The Cafe, hands down. And considering the quality of the food, the prices are very reasonable. Some see it as more of a "foodie" type place -- the dishes tend to be a bit fancier than you're standard American food joint. They try to locally source their food. High quality midwestern cuisine. They don't take reservations, so be prepared to wait a long time during normal dinner hours on a Friday or Saturday.
It's tough to choose, because there is some great pizza in Ames in a variety of styles.
Great Plains Sauce & Dough Company -- unique crust, one of my favorite pizza places.
Black Market Pizza -- If you want Chicago Style, this is the place to go.
Jeff's Pizza -- The best of your standard New York style pizza joint, and they have some tasty and unique toppings
Vesuvius -- This pizza is really, really delicious. It's very thin crust, but not New York style. It's actually about as close to real Italian pizza as I've had in the States.
I don't mention Old Chicago here mostly because they're a bigger chain.. pizza and food is still good though.
Others to Consider:
Hickory Park is of course the Ames landmark.. very healthy portions for a small bill. Decent American barbecue food.
I agree that Wallaby's is an underrated place. Decent sports bar.
Fuji has a really affordable lunch special that is still available on Saturdays. Good sushi, IMO. Honestly never went there for hibachi.
Olde Main Brewery -- For a local brew or their Sunday brunch, I'd make a stop. Can't recommend them for dinner, though. In my experience the food is very mediocre for the price.
Dublin Bay -- I really, really wish this place was better than it is. Unfortunately, my experience has always been so so with the food. A cool atmosphere for the bar though.
A couple other posters have mentioned a Thai restaurant or two.. I believe Thai Kitchen is in campustown? Anyways, I've heard very good things about them.
Hickory Park is so overrated. It's not horrible but I don't understand the people that wait damn near two hours for it.
McDonald's, Burger King, Wendy's, Taco Bell...
Wallabys has slipped in my opinion. Its notthing special.
Horray drunk phone typing