This is a continuation of an LA-area post at http://chowhound.chow.com/topics/790765 in which KilgoreTrout said he and his boss are coming west to prove to the boss that East Coast tacos can't hold a candle. They're planning a day in TJ solely to eat... so if you're reading this, please chime in!
Now then... descriptions rather than addresses are included here (don't forget to make sure you can take your car into Tijuana, or your taxi bills will pile up pretty quickly) because it's a pain in the arse to try and figure out where things are by the address. Google Maps is getting better, but...
1. Tacos Salceados, Ermita Norte 30A, La Mesa, Tijuana. On "Ermita Norte" between Diaz Ordaz and Benitez López / Paseo de los Héroes. Taxi drivers know it as "Tacos La Ermita".
The best tacos in Tijuana. Quesatacos—mozzarella cheese laid directly on the flat-top and toasted brown, then stuffed with ingredients (the default is steak and shrimp, but you can get any filling as a quesataco), rolled, and put into a tortilla and sauced. The guy is a former saucier in a fancy restaurant and makes the most amazing array of sauces—hibiscus flower salsa, anyone?
2. Tacos el Poblano, Diaz Ordaz 7813, La Mesa (5 y 10), Tijuana. On the main road past the Hippodrome a few km.
Carne asada. REAL carne asada. Not the crap they steam to death this side of the border.
3. Tacos Fitos, Guadalupe Victoria, Zona Río, Tijuana. Behind Mercado Hidalgo (worth the stop on its own) between Sánchez Taboada and Paseo de los Héroes
The fastest taqueros in Tijuana—seriously. Beef birria or tripe, those are your two choices. I don't like tripe, so I always get birria—and damn, they're good.
4. Tacos Franc, Sanchez Taboada and 6th/Flores Magon, Zona Este, Tijuana. Near-ish downtown, east of the club district, three blocks east of Revolución on 6th and behind the Zona Río Costco. Walkable from "downtown".
Another specialist, this time in late-night al pastor. Blows even Tacos Leo away.
5. Tacos el Mazateño, Del Tecnológico and Popotla, Tomás Aquino, Tijuana. On Del Tecnológico (the road that goes out to UABC, the Universidad Autónoma de Baja California), at the five-points intersection of Popotla and Rodolfo Gaona.
There is but one thing to get here: camarón enchilado (chile-spiked shrimp). It's amazing.
6. Mariscos Ruben, Quintana Roo and 8th/Miguel Hidalgo. Two blocks south and half a block east of Tacos Franc. Walkable from "downtown". Five blocks east of Revolución.
Seafood. Oh my God, the seafood. Mexico's seafood is tenfold better than San Diego's, and barely any of it makes it across the border. Yes, it's a truck, but they are the best seafood tacos in all Tijuana. My mouth waters just thinking about it.
There's a lot more—a LOT more—but this should get you started. I hope others will contribute.