As a general recommendation, look for the "Denni Menu" at restaurants, which is the menu of the day. You can often find really great deals on classic Czech dishes. And avoid the restaurants right on the Old Town Square - though a great setting, they are really overpriced and the food was not recommended by locals (or Rick for that matter).
We ate at Restaurace V Cipu II (the one on Michalska, just a little bit away from the Old Town Square, there is another one in the new quarter). The food was excellent, traditional Czech. And like a lot of places in Prague, it was very inexpensive - we each had a couple of drinks, shared an app, had our own entrees, and the check was less than $30 USD, maybe even $25.
We also really liked the Klasterni Pivovar, right across from the Strahov Monastery, in the Castle Quarter. Make sure you go to the Pivovar, not the Restaurace (which is more touristy). The pivovar is a brewpub, with excellent beers, great food, and a nice patio.
We too ate at Lokal, which was very good. A bit trendier and a bit more expensive, but still great Czech cuisine, and it's Prague, the prices are cheap.
Definitely try to grab a beer at U Zlateho Tygra, if you can find a place to sit. It's a traditional Czech pub, only one kind of beer on tap (Pilsner Urquell), filled with smoke, but it is such an authentic, awesome atmosphere. I'm quite certain we were the only ones who didn't speak Czech in there. They just keep bringing you beers until you say you don't want anymore. Pres. Havel brought Pres. Clinton here when he visited Prague in the 90s. We didn't try the food.