When I say "Mexican Subway" I am referring to the type of restaurant, not some sort of Tijuana underground.
Restaurants of this type that I have encountered are Qdoba, Chipotle, Baja Fresh, Panchero's, and Moe's.
Qdoba is the classic to me, just because it's the first one I went to. Great soup, great huge burritos, tacos, and everything. Really thin tortillas that are either terrific or awful, depending on who you are. Also, their new Mexican Gumbo item is the shit. It's basically the guts of a burrito under soup.
Chipotle was ok the one time I ate there, but that was while I was very hungover and the morning after I had made out with a very fat girl, so my memories aren't that positive. They did have several flavors of Tabasco, which was cool. There are almost no Chipotles in my area, which is weird considering they seem to be the dominant force everywhere else.
Baja Fresh is another regular place for me. I'm not a big fan of their menu items, but you can pretty much put together whatever type of burrito you want, so that's cool. Their chips are consistently stale and bad, though. Awesome nachos, though - I guess you can't tell the chips are stale when they're under a pound of cheese and meat and beans. I've never had their soup because it's scary looking
Panchero's is pretty decent. Their meat is pretty flavorless, which is weird because you can watch them grill the chicken and it's obviously marinated in something. I'm not a big fan of their tortillas, which are a bit more substantial than qdoba's, but it's pretty decent overall.
I tried Moe's for the first time last night - I don't think I'll be eating there again. The tacos were so messy I had to eat them with a fork, and the chicken was just shredded shit that tasted like it had been soaking in warm water for a few hours. It may have been because I went there late, but it was crap.