There are many tours in Prague, particularly of the walking variety, with some focusing on a particular area/activity in Prague (like Haunted Prague Tours). Out of the numerous websites offers a large selection of tours for choice.
Another tour organization of particular note is City Bike (+420 776 180 284). The original and the best, this company offers daily bike tours and even offer family bike tours with kiddie bikes and baby seats. Tours include city based ones, castle orientated ones and private tours. Prices start for 540 Kc.