Cheap Non Touristy Hotels
Here are some nice hotels in Prague that give you a great launching point for exploring quaint areas where tourists are rare but welcomed. You can access famous Prague attractions like the Charles Bridge and Castle by tram and underground metro but you will be glad to return to your quiet little part of town where you’re not just another tourist in the crowd.
Since all the recommended Prague hotels are near the River Vltava, inquire about catching a boat to one of the islands like Císařská Louka, known as Fun Island, where you’ll find an oasis of nature amid the city with great picnic sites, playgrounds and even a (I've never done it) paintball arena.
Hotel Andel
Far from the crowded tourist sites, the Hotel Andel is positioned in a quiet business neighborhood within walking distance to the historic city center, which you can also reach via the underground metro. The rooms are top notch with homey touches like wooden floors and marble wash basins along with Wi-Fi and flat screen plasma TVs. If you spend a day exploring nearby Císařská Louka Island you’ll be glad the hotel has a washing machine you can use while enjoying your free breakfast at their restaurant
Arpacay Hostel
A backpacker’s delight, the Arpacay Hostel in the non-touristy Smichov district takes budget travel to whole new level with a free breakfast, big shared kitchen, security lockers, comfortable beds and free Wi-Fi throughout the four- story building. You’ll find clusters of restaurants and entertainment venues at the nearby Andel underground metro station and quick passage to other points of interest. Take a stroll through Santoska Park with its beautiful old trees, climb up the Lookout Tower and enjoy the tranquil atmosphere at the Strahov Monastery.

Emma Apartments
Like a home away from home, the Emma Apartments offer you clean, bright, apartment-style double rooms with personal kitchenettes and private bathrooms complete with hair dryers. Take a 15 minute walk the historic city center or sign up for their free city tour to get the low down on the Old Town district. Check out the Polish beer gardens and international restaurants frequented by the locals in a neighborhood dominated by a beautiful park that includes the Folimanka Sport Hall that hosts not only competitions but concerts.
Miss Sophie’s
Situated in the New Town district near one of Prague’s many universities, Miss Sophie’s fosters the collegiate spirit of international camaraderie with their non-smoking brick cellar lounge and big communal kitchen. You’ll find this off-the-beaten-path hostel has clean dorm rooms with secure lockers, internet access and private bathrooms. Purchase breakfast before you take off to explore the cobblestone streets or just ask the friendly staff which nearby café they recommend. Find great little hideaways frequented by ex-pats who can give you tips which nearby bookstores with reading material in your language.

Down Town Suites
Expect more at the Down Town Suites with spacious apartments with one or two bedrooms, modern kitchens and even a living room. Private bathrooms have bath-tub arrangements and even a bidet. The homey atmosphere doesn’t mean you sacrifice hotel services, though, their restaurant serves free breakfast and the cozy lounge is a great place to make friends while you do your laundry in the onsite washing machines. Just a tram stop away from the city center, you’ll get a great taste of Prague’s local charm in this quiet neighborhood lined with baroque buildings full of charming shops and restaurants.

Booking a cheap hotel in a Prague neighborhood gives you a chance to live like a local while still having access to the great tourist attractions.
The above are my recommendations. Want more? Find more visitor reviewed and recommended Prague hotels.
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