PJs and Citrus City were nice, but when you say best "affordable" I'm not quite sure of your range. Those are some of the more $$ for Orange, but not expensive when compared to say, South County.
Watson's and Filling Station are good if you want a "Pleasantville" type setting, reminds me of Happy Days. Not a bad thing if that's the type of place Dad likes. Rutabegorz is a converted house that is cramped and kinda shabby, but has some darn good grub.
I admit to enjoying Felix Continental. Location, price, and food overall are great. Folks might disagree about it being the "best". I also thought the place right next to the University was pretty good (Papa Hassan's?). Is that still there?
I'm not as familiar with that area, but of the places I've tried, I can recommend:
Arthur's Restaurant (for breakfast or lunch)
240 N Tustin St
Tulsa Rib Company (for BBQ)
954 N Tustin St
Jagerhaus (for excellent German food)
2525 E Ball Rd
I haven't been to this place yet, but have heard good things about it and have been meaning to try:
Steer Inn (for steaks)
801 S Tustin St
Here is a review on the place from the Elmer Dills website:
All suggestions made so far are good. Watson's has been around since 1899 but they froze in time somewhere around the 1940's or 1950's. You could go somewhere else for your meal then go get a malt or a shake at Watson's. Just around the corner from Watson's is a new up-and-coming Mexican restaurant called Gabbi's:
Caffe Lucca and Rutabegorz on Glassell. Citrus City Grille and Byblos are great too. I do not recommend Felix Continental, you might be tempted because of the great location (right smack at the circle) but lately it's been blasted here.
The Filling Station is an institution as well as Watson's drugstore (great breakfast and outdoor seating)
If you are in search of a great dive bar, O'hara's pub rocks!