I have a little prototype with an ARM processor and a compact flash reader, I have attached the compact flash from my digital camera and Linux mounts it using vfat filesystem.
I don't want to use the memory with the camera anymore, so I'm wondering which is the best filesystem to avoid wearing out the flash memory.
Compact flash does automatic wear leveling so I would not worry about it too much; which one is "best" (in this case meaning the one that does the fewest writes to update metadata?) probably depends on your access pattern. I would expect little difference unless you are using the flash card as a Usenet or email spool with thousands of tiny files.
Mounting the drive with "-o noatime" is likely to make a much bigger difference than choosing between filesystems.