I finally visited the Central Archive for the History of the Jewish People (CAHJP) in Jerusalem.  I went over the (not computerized) card catalog and made a list of material which might be helpful for researchers of Bohemian and Moravian Jewish genealogy.  Note that I didn't list all the material found for some reasons:

• It would have taken me many days 
• Much was written in German ( which I don’t read) 

       I'll use some abbreviations:

• CKB =  the CHEVRA KADISHA (burial society) book 
• SB    =  the Synagogue book (with order of sitting places etc..)  
• CB   =  Community book  
• MB   =  MOHEL book (circumciser book)  

       Here is the list for Slovakian, Czech and Hungarian records:
..

Beled ..............................	- Birth records 1886-1895; Death records 1890-1
Bratislava ......................	- U:berreste aus dem gemeindearchiv von Pressburg (18-19 centuris) - Stammbaum des JOSEF FICSHER in TYRNAU Erinnerungen (1872-) 1891-1902
Breclav ...........................	- SB 1855 - CKB 1870-1906
Boskovice .......................	- SB 1814-1841 - CB 1741-1780
Brno .................................	- A customs receipt of Shimshon Eybshitz
Cliscauti (in Bessarabia) ...	- The GERSTEIN family
DeutschKreuz ..................	- CKB 1849-1938
Dolni Kounice ..................	- CKB 1858
Gajar ................................	- MB 1843-1883
Golcuv Jenikov ...............	- Rechnungsbuch der Israelitische schule - few pages with matrikals : 1897-1921; Yahrzeit 1847-189?
Holesov ...........................	- Documents of the ERLICH family
Kutenplan Bei Marienbad ..	- Cemetery photos
Kounice ............................	- CKB 1721-1858
Nove Mesto n. Vahom ....	- CKB 1845
Nachod .............................	- The MAUTNER family 1786-1997
Nadas (today Trstin) ........	- A birth certificate of Max ERLICH, son of the rabbi Jacob Erlich
Nagy-Kanizsa ..................	- CKB 1792-1906
Nove Zamki .....................	- Uberreste der aktander kultusgemeinde:…..listen… 1879-1950
Novy Kolin ......................	- MB 1771-1819
Prostejov .........................	- Copies of tombstones marks (or inscriptions?) until the 18th century - SB 17-18 centuries - CKB 1705-1773; 1725
Rousinov (Neu-Raussnitz)...	- CKB 1701 - SB 1701-1852 - CB 1701; 1899, 1930 - Correspondance 1808-1890 - Militardienst 1840 - Familien - Anzahl der Jud. Gemeinde (18-19 cen.) - Grundbuch mit namensregister (18-19 cen.) - …..families….1781 - Competentenbuch    1809
Sopron ..............................	- A Soproni Zsido temetok to:rtenete
Trebic ...............................	- CB 1803 - CKB 1837
Trnava .............................	- Tombstones inscriptions (from the local library)
Turka - Luka ..................	- CKB 1899
Usov ...............................	- Genealogy of the LOWY family (early 18th century)
Verbo (Vrbove) ..............	- SB 1777-1844
Volyne .............................	- Autobiographical notes of Dr. LEDERER with genealogical lists 1974
Zaluzany ...........................	- 3 photos of tombstones 1973

       Regarding PRAGUE - there were many records but, as far as I could see, the source for all was the Jewish museum. Regarding the private documents from Prague, here is a list of  some of the families whose documents can be found there: GERSTEL, TAUSSIG, WEIL, REACH, PORGES, ZAPPERT and WELTSCH. There is also genealogy of the KNINA family. Some of the above mentioned material was from Czech Museums. (Brno Museum If I'm not mistaken).

       I hope it helps.