Czech Beer -- Prague

Seemed like any place with decent food served decent beer. But if you are interested in a big beer bust, the Brits do seem to enjoy beer in Prague:
http://www.prague-guide.co.uk/stag-parties-in-prague/
...for large stag parties coming to Prague is to stick to the bigger pubs, and avoid smaller ones. The Irish bars located in the city centre are also a good choice. You can also try the Dragon Pub on the Old Town Square, the Three Lions pub in Krakovska and many others. As long as you come early, and unless you are totally drunk or aggressive, then you should get in. Many places are keen to try to balance girls and boys, so if you can you should bring members of the opposite sex in with you.
Hen Parties
If you are planning a hen party in Prague contrary to the stag parties you will be absolutely fine. Even very large groups of women can go almost anywhere without problems. The most popular places for hen parties are disco La Fabrique and Bombay Cocktail Bar.

My favorite places to enjoy a Czech beer are the lower level of the very art nouveau Municipal House and a nice table along the river on the Kampa Island side (after crossing the Charles Bridge). We haven't found these areas to be crowded or smoky. Our absolute favorite beer to drink was a quest for "pivo z tanku". This is unpasturized beer that hasn't been exposed to air. We found our best experience one evening just wandering up Mosteka (the Charles bridge street) towards the castle but stopping at the first large square. There was a restaurant on the east side, half way down the street that had a hand lettered sign outside advertising that they had pivo z tanku; creamy, smooth, cold and delicious.

EDIT: the restaurant is at the end of the block, not middle, and says "Pilsner Urquell Original Restaurant" above one of the arched doorways. I can see it on google street view so PM me if you want more help finding it.

I don't recall having smoke issues in 2010. I did recall back then that the non-smoking section one of the more popular restaurants was significantly smaller than the smoking section.

The good news is that the Czech Republic is or will soon be in compliance with EU smoking rules:
http://www.reuters.com/article/us-czechs-smoking-idUSKBN0OJ20L20150603

The Czech government approved a draft bill to ban smoking in
restaurants and bars and move the country into line with restrictions
in place in much of the European Union.

The Czech Republic is the last EU member to allow unrestricted smoking
in restaurants. Past governments have tried to enact such restrictions
but run into opposition.

The draft bill must still pass parliament before it can be signed into
law by President Milos Zeman, himself a regular smoker.

A quarter of Czechs smoke, putting it just below the EU average of 26
percent, according to Eurobarometer.

"With this law, the Czech Republic will embark on a path where the
majority of advanced western European countries have gone a long time
ago," Health Minister Svatopluk Nemecek said after the center-left
cabinet approved the measure.

Two great places for beer with a view...
The outdoor deck behind the Museum Kampa (the modern art museum) right on the Vltava River across from the old town. Can be crowded in summer but hold out for a table by the water and it's totally worth it.
The other place is the Grossetto Marina which is also on the river but on the opposite side. It's in an old barge that has been renovated with a great outdoor deck facing Castle Hill.
No smoke that I noticed!
Beer is cheap...I don't think I paid more than about $3 for 1/2 pint anywhere in the CR. Some places out of the city I paid as little as 75 cents. Mostly it was about $1.50.

http://www.praguebeergarden.com/
this website is great for info about places to enjoy beer and there is a section just about beer gardens.
I have 2 favourite beer gardens, Letna has stunning views and is massive never had a problem getting a table,no real choice of beer and the snacks are limited, there is however a restaurant within the beer garden if you want a decent meal.
Riegrovy Sady is a great place and has a wide choice of beers though you have to go to each individual kiosk if you want to try the range/decent snacks there mainly sausage based and they have a big screen tv for watching sports and sometime have live music on, can get real busy but folk are very good about shuffeling up to make room at tables.
In the better weather many places will have outside seating ,some are better than others.
as has been said there are many barges/boats on the river were you can sit out and in the area called Naplavka there are a few small bars that open up in the summer months and set up tables an chairs over looking the river.
Smoking is not so much of a problem now, as has been mentioned a no smoking policy will be introduced but many bars have already implemented a smoking ban.
my favourite place to drink and have a meal , sorry too many too mention but for a summer days lunch outside the the Pivovar marina Holesovice ( http://www.pivovarmarina.cz/ ) hits the spot for me, can be difficult to find but worth the effort, lovely outside tables , decent food and they make their own beer, staff are realy nice and they will get an English menu for you if you ask. all the staff speak some English many speak it very well.

sorry never answered my favourite beer
Uniticky, a fairly new micro brewery to the north of the city, it is as far as I am concerned the best pilsner style beer out there and better that the original, becoming more and more popular and the brewery has expanded a fair bit recently, you can get out there quite easily and they do pretty good food, staff are nice, and speak good English, the owner of the restaurant used to live in Ireland for many years.they have a decent outside eating drinking area but every time I have been there it has been raining.
http://www.unetickypivovar.cz/