My husband and I had only a couple of days in Prague, but really enjoyed the city. The historic center is beautiful, and the Prague Castle complex should not be missed. Don't be put off by the tourist shops in the city center, but I wouldn't waste my time eating anywhere with lots of tourists. Just walk a little ways, and you can easily find pubs and cafes serving fine beer and hearty food.
Our two favorite places were:
1) V Zatisi was impressive. It managed to keep true to Czech roots, while executing dishes in a modern, dare I say, "international" style. We had a 5-course tasting menu with matched wines, and spent about $150. It was really excellent! Dishes change seasonally, but we had rabbit and venison main courses that were superb. The friendly wait staff knows the wines and will match effortlessly. All speak English perfectly, even the Scotsman! It can be a little hard to find in the dark, but just keep walking.
Oh, and don't be put off by the phrase "late-harvest" on all the wines, it doesn't mean a sticky or port.
2) Jan Paukert (Narodni trida 17; 420-224-222-615; www.janpaukert.cz) : Finally a place with no English menu. It is just cool—looks like it was renovated in the 30’s. Pick your open-face sandwich or 2 by pointing. Then pay, take your cafeteria tray, and walk to the back room, where you can go to the bar and get a beer or a lovely flute of Czech sparkling wine!
It is on a large, well-travelled street, but you must walk away from the department stores, etc. When the shops get smaller and there are fewer English signs, you'll be getting closer.