I've been to both and I would recommend both. In terms of deciding between them, I would probably plump for Prague just as it is slightly cheaper (not as though I found Berlin especially pricey) and I think the nightlife there is more of a departure from the UK than Berlin (from what I've seen). When I was in Prague I went to this crazy warehouse-type club where you pay to get in and then it's a free bar (girls get in free), got caught up in the middle of an ensuing rap battle, was casually groped by some Asian girl who didn't speak a word of English whilst actually dancing with my girlfriend at the time and we drank far too much from the limited selection of drinks they had on offer (martini, whisky and vodka) and mixers which they eventually ran out of. Having said that, there are loads of cool bars and clubs in Berlin as well (Madame Claude is a good one in Kreuzberg - lots of furniture is bolted-on on upside down on the ceiling of the bar) and Germans party ridiculously hard with clubs generally open way later than most are in the UK.
Culturally, I found Berlin more interesting to walk around (lots of cool graffiti, interesting back streets etc.) but Prague is more conventionally pretty and romantic. I also preferred eating out whilst I was in Prague. To be honest, I would just toss a coin and go with whichever, they are both cities you definitely should visit.