Just returned from Prague.
I felt everywhere was safe. Area around Wenceslas Square, and Old Town Square known for pickpockets, but otherwise OK. Lots of people out at all hours. Of course they were celebrating as Czechs won a series of hockey World Cup games. This was he first time I'd been able to spend significant time in Prague - quickly coming p in my list of favorite cities!
Budapest is a bit rougher, but still OK. There is an actual "blacklist" of bad establishments in BP put out by the US Embassy there, but I doubt they are the type of establishments your GF might be frequenting.
Good BP site -
http://www.budapesthotels.com/systempages/info.asp