All Czech archives are publishing the registries (parish books) online nowadays. The first archives to start was the State Regional Archives in Trebon in 2008 and was followed by the other archives during the following years. Not all registries are available yet, but they should be available in few years time. Here are the links to the digital archives (with comments).
Prague City Archives: http://www.ahmp.cz/katalog/
Available partially in English, the Inner Prague has quite many parish books online, outer Prague only some of them. As the website is not whole in English, I'll prepare step-by-step guide how to find the registries (I hope it will not take me long time to do so).
State Regional Archives in Prague, State Regional Archives in Pilsen, Moravian Land Archives in Brno: http://www.actapublica.eu/
Available in German, but not yet in English. I have create a guide to the older version of the archives, but it is not valid anymore. I'll prepare new guide soon.
State Regional Archives in Litomerice: http://matriky.soalitomerice.cz/matriky_lite/
Available in English (however the description of the parish books is in Czech). You need to know what means which word and so on, so I'm preparing a small dictionary of words used in Czech archives.
State Regional Archives in Trebon: http://digi.ceskearchivy.cz/
Fully available in English. Definitely the most user-friendly website, offers not only registries, but also censuses, chronicles and much more.
State Regional Archives in Zamrsk: http://vychodoceskearchivy.cz/zamrsk/matriky/
Well, well, well... This is a bit more complicated. The registries are not available to be browsed online, you have to download them to your computer in zip file, unzip them to your local folder and then browse. So you should be sure that the registry you are downloading is the one you really want. A bit complicated, right? I'll prepare separate article about it.
Land Archives in Opava: http://matriky.archives.cz/matriky_lite/
It has the same system as archives in Litomerice. It is in English, but the descriptions are in Czech. Again, small dictionary will help. Let's hope it will not take me a lot of time to prepare it.
Please remember: not all parish books are already available online. It can happen that you will not find what you are searching for and you'll have to wait until the archives publish it.