The view at night from the bridges across the Charles river back towards the Castle side is amazing. It's actually better from the bridge that the trams run on, not the Charles Bridge...

On the Mala Strana side, near the embassies, is a great little cellar bar called St. Nick's, I think. There are also a bunch of good bars/restaurants that aren't too touristy near the Ujezd tram stop on the 22 line.

IMO, Gambrinus and Budvar are the way to go w/ beer, and Velvet is pretty good too. There are a lot of side streets good for wandering, and free/cheap concerts can be found at night in many of the churches around town.

There's also a small but nice casino at the Hotel Imperial near Old Town Square where you can play for hours on relatively little money.