Externally use the FAT32 as is the most extended system on USB sticks, Memory as SD, MMC, Compact Fash, etc.
this is for interchange information with other systems.
Internally use his own partition and encripted system that only has sony know how work, there is no way yet to view the content of the internal disk outside the PS3. (and iniside the PS3 we show trought the XMB)
Regards
Spirax