Lehka Hlava is a great vegetarian restaurant at Borsov 2.
http://www.lehkahlava.cz/en_novinky.htm
It's definitely one of those vegetarian restaurants that is doing such interesting things with food that non-vegetarians like it. And the prices are extremely reasonable, so it's cool to do a lot of different things there.
There's a great Czech restaurant on the side of the Vysehrad hill towards Nam. Miru...I don't know the name of it, but I can tell you how to get there if you want. No tourists this time of year.
P.S. Make sure you have some Pilsner. And Gambrinus. Budvar is pretty sweet.