Although it's a local chain, I just thought I would put in a nice word for the folks at the Not Your Average Joes in Watertown. Mw four year old is a huge fan (eg. we are not allowed to go out anywhere else if he is with us) and the staff there is great with the kids. The adult food choices are generally standard diner fare at restaurant prices but are almost always perfectly executed, delivered fast and they keep the beverages coming. The best part - we virtually always sit at the pizza making station - the kids can get a piece of dough to play with, we watch the pizzas made and cooked in a huge open oven, and can actually have an adult conversation 'cause the kids are occupied.
BTW the pizza is great. Thin, chewy crust, interesting toppings with unusual flavors (hoisin sauce with onion and chicken as a special one night was particularly good).
We've tried the Joe's in arlington, also, but it is more adult oriented and has no seating at the pizza bar. The staff there is also kid friendly but the wait for a table tends to be long.