I don't have anything to add about the Old Town places, but there are a few others in SD that might be worth checking out. First is Fidels
Fidel's Little Mexico - San Diego Entertainment Guide at SignOnSanDiego.com. They have one in Solana Beach (on Stevens) and one in Downtown Carlsbad. Personally, I think the one in Solana Beach is way better. Their carnitas are fantastic! Plus it is built on multiple levels (it used to be Fidels house) so it can be fun to wonder through. Also good is El Callejon in Encinitas
Restaurant - Home Page. Small place, but good food, good drinks and good time. Simple food, its not drowned in toppings and sauces. They have a chorizo & cheese dip that is amazing. Lastly, no trip is complete with a visit to Los Cuatro Milpas
Las Cuatro Milpas - San Diego Entertainment Guide at SignOnSanDiego.com It is kind of a hole in the wall, and is not a restaurant, but man do they have the best tamales, beef tacos and tortillas! If you want to bring home tortillas, you have to call ahead to order them so they can make them. Trust me, its worth it!