There is not really a stilistic and thematic unity to the films (as you have probably seen), but what was special about the Czechoslovak new wave was the fact, that they all somehow worked together. Not all directors (and crew) graduated from FAMU, but (even the older directors like Kachyna, Vlacil, Jasny...) worked with similar crews, often the directors of one film were assistant directors of the other. Some were fighting with the censors to get others films made, etc.
Many of them were also in the surrealist tradition of Czechoslovakia (well the Slovak was a little later, I think it started in the thirties, whereas the czech came a little earlier...unfortunately it is not very well known, even though it was equally important as the french movement...but people in the west are mostly arrogant toward slaws (and hungarians)).
Czechoslovak New Wave
Central-European Cinema...both by Peter Hames
The Cinema of the other Europe by Dina Iordanova
The Coasts of Bohemia by Derek Sayer (doesn't deal with film, but I find it an important book considering the evolution of national identity and art)
Geopolitics of Central-Europe by Oskcar Krejci (again...not about film, but a book I think everyone interested in the region should read, and all people from Germany and Switzerland (so they gain a better and less arrogant world view)) It's also a good book to help understand the tensions/differences between Slovaks and Czechs. (this one is downloadable for free)
Hope this helps.
Also if you like teen-movies, the "Basnici" series (the first three films form the series) are very good. That is how films about teens trying to loose their virginity should be:).