I was just in Prague for New Years. It's a nice city, if not a little overrated, or at least that's what my friend and I said while there. One thing that may sound stupid but is great is to just stroll around, especially the Old Town, Charles Bridge, and Prague Castle areas. Tons of little shops, cafes, restaurants, and pubs. I don't have any specific pubs to mention, but if you see a place and think "wow, that looks like a hole in the wall", it may be, but it may turn out to be the best time of your trip, as we found out. Prague has GREAT CHEAP beer, and Czech beer is, of course, amazing. Honestly, just buy a metro ticket, take the trams and subways and just find your own ideal place. It's a nice, safe, and affordable place full of culture and history. Enjoy!