I can either use Berkeley DB or FSFS, which one should I use? I'll also be using the repositries on my windows XP machine with TortoiseSVN
FSFS is the "new better" file system for SVN. DBD was the original file system, but FSFS was devloped for a reason and is now the default file system for SVN.
FSFS is more stable, more backup friendly and has been around for a while to be considered stable and mature.
Read the link in Archimedix answer for an official comparison.