Subway is your healthiest fast food option. If you drive through somewhere or order to pick up, order a salad - make sure there is no breaded chicken and use a vinaigrette dressing - no ranch, bleu cheese, thousand island, etc.
If you aren't wanting a salad and you must have a burger, somewhere that charbroils is going to be healthier - Burger King, In N Out, & Jack In the Box all charbroil their burgers (be sure to get no mayo to dramatically cut down the calories) and order a side salad instead of fries. If you go to Wendy's, order chili and a salad or a baked potato with a salad - those are both low fat options as well
If you go to Taco Bell, order al fresco style to cut down on the fat and calories. Arby's roast beef sandwiches aren't too bad for you either - it's the fries that throw the meal down the drain (nutrition wise)