there are loads but here are a few i have been in recently some as recent as last month.
https://www.facebook.com/beertime.pub/
specalist beer bar but does half decent food and has a cheap lunch menu, nice outside courtyard to sit in.
http://peronsmichov.cz/
this is a real favourite of mine ,great food with a cheap lunch menu and I think the only place in the city with Radegast beer from the tank, real quirky courtyard area to sit in.I am often in there for lunch as i ahve agood friend that works nearby.
http://www.kozlovna.eu/en/
another favourite of mine and again cheap lunch menu.Kozel beer from the tank,service can be a bit patchy but generally good.
http://www.potrefenahusaandel.cz/
this one is at Andel and they have several others in the area,part of the Staropramen brewery pubs, good food and decent beer ,service is always pretty good and the food very nice.cheap lunch menu available i think.they hace a place to the Brewery just a few hunderd yards from the one at Andel.I have been in loads of Potrefena Husa places all over the city, indeed all over the country and they have all served up pretty decent food.
The cheap lunch menus I mention tend to only be in Czech though some places may have an english translation (I think Peron does),these are all mid range type places , nothing fancy but not the low end places either.
seriously there must me over 100 places in the general area of Smichov/Andel