Prague is divided into 10 districts, so for each category ( Restaurants, Bars, Cafés, Clubs), I listed the places by district, Prague being a big city, people usually look for places by area.
This is my work sheet for this trip, a list that comes from people that I questioned or from blogs that I read through, the comments on the side of the names are those that locals made.
I decided to publish this list because in 4-5 days I can’t try out everything and it might be that I missed out on something special; in any case, the locals to whom I showed this list were impressed with its quality, so it shows that I was given good advice.

A map for good deals:

https://mapsengine.google.com/map/u/0/edit?mid=zMQkPD73Yzvw.kM97OsgHkiIQ

 1) Restaurants
Dishes : If you want to try a typical czech dish, then it would be Svíčková, Řízek or for sweet dishes Plněné ovocné knedlíky. (try to google it in case).

Prague 1

Beas Dhaba (indien)
Týnská 19,
110 00 Praha 1
Tél : +420 608 035 727
http://www.beas-dhaba.cz/

Bistro (they have some home made cakes)
Králodvorská 16
110 00 Praha 1
http://www.praguebistro.com/

Estrella (veggie, I highly recommend this one!)
Opatovická 159/17,
110 00 Praha 1
Tél :+420 777 431 344
https://www.facebook.com/estrella.rest

Grossetto Marina ( a chic italian on a boat, I met a couple that were happy they went for a romantic dinner but admitted it was chic), looks a little snobby. 
Alšovo nábřeží
110 00 Praha 1 – Staré město
Tél :+420 605 454 020
http://www.grosseto.cz/

Hôtel U Prince
Staroměstské náměstí 29
110 00 Praha 1
Tél : +420 224 213 807
https://www.hoteluprince.com/hotel-fr

Jina Krajina
Řeznická 1890/4,
110 00 Praha 1-Nové Město
Tél :+420 222 231 148
http://www.jinakrajina.cz/

Klub architektů
Betlémské náměstí 169/5A,
110 00 Praha 1
Téléphone :+420 224 248 878
http://www.klubarchitektu.com/fr/

Lehká Hlava (végétarien)
Boršov 280/2,
110 00 Praha 1
Tél : +420 222 220 665
http://www.lehkahlava.cz/

Maitrea
vegetariánská a veganská restaurace v centru Prahy, Týnská ulička 6, 110 00 Praha 1
http://restaurace-maitrea.cz/
I really like this place.. it’s a nice vegetarian restaurant even though I am not vegetarian:)

Restaurace U Pinkasů
Jungmannovo nám. 15/16
110 00 Praha 1
http://www.upinkasu.cz/

U Chlupatýho ducha
Restaurace, Pizza
Konviktská 6
Praha 1
+420 224 238 171
http://www.uchlupatyhoducha.cz/

Prague 2

Ahradky Park Café (Beer garden)
Rieger 28
Prague 2
Tél : +420 608 911 536
e-mail: parkcafe@centrum.cz

Bio Zahrada
Belgická 33
120 00 Praha 2, Vinohrady
Tél : +420 603 752 468
http://www.bio-zahrada.cz/

Dish (For good burgers)
Římská 1196/29, 120 00
Praha 2
Tél :+420 222 511 032
http://dish.cz/

Mlsnej kocour
Belgická 116/42, Praha 2 – Vinohrady – Náměstí míru
Tél : +420 222 541 584
http://www.mlsnejkocour.cz/

Plevel (vegan and raw restaurant – you have to go there!)
Krymská 2
101 00 Prague 2
Tél : +420 273 160 041
http://www.restauraceplevel.cz/

Sokolovna (traditional Czech meals)
Slezská 22/821
120 00 Praha 2
Tel : + 420 222 524 525
http://www.restaurantsokolovna.cz/

The Tavern (For good burgers)
Chopinova 1521/26,
120 00 Prague 2
http://www.thetavern.cz/

Vinohrady Parlament (traditional Czech meals)
Korunní 1 / Praha 2
Tél :  +420 224 250 403

Prague 3

Café Pavlač (its more a café than a restaurant but they serve nice food as well:)
Víta Nejedlého 487/23,
130 00 Praha 3-Žižkov
Tél :+420 222 721 731
www.cafepavlac.cz

Susta Strudl (strudle)
Jeseniova 29
Prague 3, Zizkov

Prague 5

Restaurace Kozlovna
Lidická 20
Praha 5
http://www.kozlovna.eu/

Prague 7

Bio Oko (more cafe then food)
Františka Křížka 460/15,
170 00 Praha 7
Téléphone :+420 608 330 088
http://www.biooko.net

Cafe Liberal « Karvarna Liberal » (more cafe as well, but nice)
Heřmanova 6,
170 00 Praha 7
https://www.facebook.com/kavarnaliberal

Prague 8

Můj šálek kávy
Křižíkova 386/105,
186 00 Praha 8
Tél : +420 222 981 874
http://www.mujsalekkavy.cz/

Prague 10

Cafe Sladkowski
Sevastopolská 17
110 00 Praha 10
http://www.cafesladkovsky.cz/

Cafe v lese (more pub/cafe but definitely worth seeing)
Krymská 12,
Praha 10 – Vršovice
http://cafevlese.cz/

Jiná krajina
Kodaňská 319/5 (vchod z ulice Moskevská)
101 00 Praha 10
http://www.jinakrajina.cz/

Bars

Pilsen is considered to be the best Czech beer
Krušovice is good as well according to me, if they don’t have Pilsen.

Popo Café Petl
Újezd 409/19
118 00 Praha 1 -Malá Strana
http://www.popocafepetl.eu/

Prague Beer Museum
Dlouhá 720/46, 110 00 Praha 1-Staré Město, République tchèque
A good pub where you can taste different kinds of beer and meet foreigners at the same time. It’s the Prague Beer Museum in Dlouha street.

Cafés

http://www.tasteofprague.com/pragueblog/#.UzKkpK15NJl

Prague 1

EMA
Na Florenci 1420/3
11000 Prague 1
Tél : +420 730 156 933
http://www.emaespressobar.cz

Mammacoffee
Vodičkova 6
110 00 Prague 1
Tél : +420 773 263 333
www.mammacoffee.cz

Prague 2

Café Neustadt
Karlovo náměstí 1/23
12000 Prague 2
Tél : 774645659
https://www.facebook.com/cafeneustadt/info

Café Oliveira
Mánesova 1516/65
12000 Prague
Tél : 731004495
http://www.cafeoliveira.cz

Monolok
Moravská 18, 120 00 Praha 2
Rezervace: 739 018 195
http://www.monolok.cz/

Pradelna Cafe
Slavíkova 21
120 00 Praha 2
Tel.: 774 843 477
www.pradelna-cafe.cz

Prague 5

Cafe Lounge
Plaská 615/8
150 00 Praha 5
Újezd / Malá Strana
http://www.cafe-lounge.cz/

Prague 7

Erhartova cukrárna
And from confectioner’s Erhartova cukrárna ()
Milady Horákové 56, Praha 7 | Po–Ne: 10.00–19.00
Vinohradská 125, Praha 3 | Po–Ne: 10.00–19.00
http://www.erhartovacukrarna.cz

Prague 8

Cafe Decada
Vacínova 10, Praha 8 (Palmovka)
Tél : +420 774 446 474
http://www.decada.cz/cafe.php

Muj salek kavy
Křižíkova 105
Praha 8
(“B” Křižíkova, tram Urxova)
Tél : 222 981 874

Prague 10

Cukrárna Pralinka
Vršovická 866/3
101 00 Praha 10 – Vršovice
http://www.cukrarnavrsovice.cz/

Clubs
For nightlife, it depends what kind of music you like. As for disco&dance music, I’d choose

Sites
http://praguebeats.com/
http://jlbjlt.net/
http://www.digital-guide.cz/fr/poi/

Nebe
Křemencova 10
110 00 Praha 1
Tél : +420 608 644 784
http://www.nebepraha.cz/

Hany Bany
Veleslavínova 58/5
110 00 Praha 1-Staré Město
Tél : +420 222 327 602

Cestr
Legerova 75/57, 110 00 Praha 1, République tchèque
Téléphone :+420 222 727 851
(my favourite!!)
http://cestr.ambi.cz/cz/

George Nemec
I am a global brand ambassador for BECHEROVKA
My friend, unfortunately I will be out of Prague, so I won’t be able to take you out, but here is the list I just recently made for Stephan Berg. First of all, here is my phone number. If you need ANYTHING, I MEAN ANYTHING (advise, not sure about something, instant recommendations, taxi or bookings in restaurant or bars) you will ring, or text this phone number +42 077419 9984.

BARS TO VISIT:

Hemingway Bar
Cozy little place, awesome drinks and staff. Best friend of mine is the owner and he is really tough and proud at the same time about this little baby. –
awesome for cocktails, but also amazing for bottle of small boutique Champagne (houses), Rums and Absinths of course.
– let me know if you want to get here. They are usually full and need booking. https://www.facebook.com/pages/HEMINGWAY-BAR-PRAGUE/176421996751

Bugsy’s Bar
18 years open, very first cocktail bar after “velvet revolution” in Prague and still one of the top. –
cocktails are great, probably even better selection of champagnes –
those guys have got very tight relationships with some fine Champagne houses in France. – Hemingway is more down to earth, this is more “noses up”
Definitely must visit.
Pařížská 1068/10
110 00 Praha-Staré Město
Tél : +420 224 810 287
https://www.facebook.com/BugsysBarPrague

Black Angel’s
looks like a speak easy, but it is not – definitely work checking out – those guys were nominated last year at Tales for the best Hotel bar – if nothing else, then you must visit those first three bars
https://www.facebook.com/BlackAngelsBar

Anonymous (one of “new age” bars in Prague – down to earth, cool drinks, diferent, young)
Michalská 432/12
110 00 Prague
Tél : +420 608 280 069
https://www.facebook.com/anonymousbar.cz

Tretter’s
drinks are ok, but the interior is super nice – filled with weirdos, but second cocktail bar in Czech, only 5 min. from Bugsy’s https://www.facebook.com/pages/TRETTERS-NEW-YORK-BAR-PRAGUE/136062933087397
both owners (Bugsy’s and Tretter’s) got their work experience in Munich, so this was strong influence to our bar scene at the beginning.

Bar&Books
nice interior, but drinks are average – that Indian guy is taking his joint in Prague as a little hobby – there are  two bars in Prague, but if you go, you will want to go to one in Tynska Street – close to where you stay.
http://www.barandbooks.cz/tynska/

THERE ARE A FEW MORE BARS, BUT FOR TWO DAYS, THIS WOULD BE MORE THAN ENOUGH I GUESS.

Sansho – asian twist in Prague – rustic, simple interior, but food is awesome. http://www.sansho.cz
FINE FOOD AND CUISINE: KALINA – have not been there, but apparently one of the best http://www.kalinarestaurant.cz
We have got two Michelin stars in Prague as well: LA DEGUSTACION http://www.ladegustation.cz/en/#index ALCRON http://www.alcron.cz
LE TERROIR http://www.leterroir.cz/index-en.php

Weekends are very busy at Hemingway, Bugsys and Black Angels, so make sure you make a reservation at the bar for yourself.

Red Piff is awesome for food, and it’s just around the corner of Hemingway bar and BON VIVANTS.

The Petřín Hill, the trees are all in bloom, there is a great view of the castle and the whole city.
A bit different view (but also very stunning!) is from žižkovská věž (=žižkov tower) i am sure you have seen it already – it is the tallest transmission tower in town…
One other also interesting place is Vyšehrad. it is the second castle / cathedral in Prague. It is built on a rock right above the river.. there is also a cemetry of the famous Czech VIP people – composers, writers etc.
And regarding some bars.. on friday or sat. night, if you like at least some oldies songs (80, 90s music), go to Lucerna music bar (it is near Wenceslas sq = Vaclavske namesti) – i thinks it is a great place but dont come there before 11 – most people come around midnight.
🙂

https://www.facebook.com/endless.illusion.prague
Raph’s friends

Le beergarten
Na Hradbach at Vysehrad

Mercato Delle erbe: an old indoor market where you can shop for food or eat roasted fish. our version of san Miguel market in Madrid.

Via pescheie vecchie : an old street full of character, all the food stores get converted in bars in the evening, you can enjoy deep house at the fish shop. Great

Scolopendra : used musical instrumens and records, possibly the biggest vintage synth collection in the world.

Pizzeria tonino : best pizza ever, the owner opened his first restourant in Tokyo, he is the worldwide ambassador of Napolitan pizza.

Mercatino di via monterumigi : second hand store with a great vinyl selection, vintage hi-fi and a taste for 80″ clothes