You'll pay $2 or $3 for a beer at Nota Bene, and it will likely be 0.4 liter to boot, but when the food is that good, it is hard to complain. Mostly craft beer, to boot.
There was also a fun little place in lesser town. I can't recall the name, and couldn't find it on Google, but it was fairly close to Charles bridge, if I recall correctly, and they have a basement "dungeon" dining/drinking area. It's lit by candles and a couple of very dim lights. It actually takes quite awhile for your eyes to get adjusted it is so dark in there. It was a bit gimmicky, as in trying hard to push the old-style dungeon feel, but still very cool.
You may be referring to U Sudu, my personal favorite bar....circa 1995. Lots of other underground places in Prague....and if you get a chance to go to Krakow you'll find much of the same.
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