A Bed & Breakfast can be an a refreshingly personal environment to explore a new city. Though a B&B may be more expensive then traditional hotels, occasionally they are cheaper then the surrounding locations given the inclusion of a meal and the luxury of the environment.
The best search engine to find a cosy Bed & Breakfast is
http://www.bedandbreakfast.com/ or
http://www.expats.cz/prague/.
A few of good options include:
B&B Hastal Prague Old Town
Located in the heart of Old Town Prague, this B & B offers traditionally decorated rooms, air-conditioning, a complimentary hot and cold buffet breakfast, free internet access (WiFi) and even a welcome drink. There are 31 guest accommodations, all with private baths.
Address: Hastalska 1077/16, 110 00 Prague
Price: Single occupancy rate is between $39 and $89; Double occupancy rate is between $49 and $99
B&B The Bridge
Excellent prices in a historical house that has been recently renovated. Named for its location in Smichov, near the bridge Jiraskuv Most, visitors can cross the bridge to Charles Square (Karlovo Namesti) and precede to Venceslav Square. There are 11 guest accommodations with private baths.
Address: Zborovska 14, Praha 5, Smichov, Czech Republic
Price: Single occupancy rate is between 20 and 70 euro; Double occupancy rate is between 30 and 80 euro
B&B Charles Bridge Prague
A 3 star B&B constructed at the same time as nearby Charles Bridge. Free internet access, Wi-Fi connection, and breakfast are offered.
Address: Drazickeho Namesti 5, Prague 01, 110 00 Prague 1
Price: double room between $50-70; one bedroom apartment $90-130; 2 bedroom apartment with kitchen $110-180