Armand,
The definitive article on the question (IMO) is Menneisyys's blog over at the Smartphone & Pocket PC Magazine Forum:
Smartphone & Pocket PC magazine Forum - Optimizing storage card speed
(If the link doesn't work or your not a member, Google "storage card format smartphone 'Pocket PC'" and look for the pocketpcmag.com link on the first page of results.
Technical summary: It's really, really complicated and depends to a large extent on the quality of the card. The biggest impact on speed seems to come from leaving off the file allocation table backup, but you need to purchase specific software to do it. Leaving the FAT backup in, I tested my Topram 4GB card using a number of different variations of FAT(16) and FAT32 with different cluster sizes. I couldn't generate any significant differences in speed or storage space using my test method (moving a couple hundred jpegs back and forth.) I ended up sticking with FAT16 at a 64k cluster size, and that seems to work OK. Once my 4GB starts getting crowded, then I might try something a little more space efficient.
T-Man,
As noted, my 4GB Topram is FAT formatted and still running at about 3-1/2 months since the last format. I don't do a lot of I/O on it, so YMMV.
I actually loaded it up with jpegs and mp4 files just to get over 2GB used (under 2GB free space) - after doing that, the camera writes directly to the card (it wouldn't before; no error messages or anything, just ignored the setup of save to card.)