Tipping in the Czech Republic is commonly expected of foreign visitors.  Foreign visitors are expected to tip at least 10%. (N.B. This practice holds true mainly in Prague and leading tourist "meccas" such as Cesky Krumlov, not in the general countryside, where foreigners are not expected to do anything more than locals.)

Locals rarely leave a substantial tip in pubs or low-mid range restaurants, often leaving a few Crowns from the change rounding up to the nearest 10. This practice is changing as the economy grows and 5-10% tip is quite usual in better restaurants. Service here is unlike many other places in the world. Service staff is often sullen to dour (particularly in pubs and cheaper restaurants). Judge not by smile-quotients (Czech people are not used to smile at you at all times as e.g. Americans do), but by whether the order was taken promptly, the correct food was delivered, the bill was added up correctly and the food was good. Czech waiters do not routinely ask whether you enjoyed your meal or if everything was to your liking, however it is becoming quite usual in average-good restaurants. Sometimes, if tourists try to indicate they really enjoyed their meal or a particular dish, they are met with absolutely blank ("Little Orphan Annie") stares, as this practice is a bit foreign to a lot of Czechs.

In many traditional places, you'll see the waiter jot down your order on little paper slips which he leaves on your table. Don't mess around with it because many times it's the only record of what you ordered.

When asking for the bill, the waiter will usually wait by your side until you pay, especially if you ask to pay separately (quite common, see below).

Credit cards are somewhat new to the majority of the country, with the exception of Prague and other major cities, and tipping by credit card is considered undesirable, as many establishments will take some, if not all, of a credit card based tip "for the house" rather than passing it along to the server (actually, not many restaurants offer tipping by credit card).  If you are paying by a credit card, give the server a tip when he returns your paying slip, or if paying by cash just round up the bill as you are paying. You can also leave money on the table although rounding up when paying is much more common - just tell the waiter the total amount he should give you change for.

It is quite common for every guest to pay his bill separatly, in some cases, the waiter will ask you to pay at the cash register, often resulting in a queue. 

BEWARE: As of 2006, some restaurants in Prague have begun putting little disclaimers stating "Service is not included" at the bottom of the guest check. THIS IS UNTRUE!  By Czech law, service IS included, but a TIP is not included. Hoping to confuse unknowing tourists and guilt you into leaving (by local standards, obscenely large) tips is what this newest con is all about. Stick to the guidelines posted above. And never, ever reward bad, rude, sullen or sneery service! Doing so makes it harder for everyone and does nothing to help people here learn that tips are a reward, not a right!