Is there any tools to defrag a fat32 filesystem
 

I know Linux doesn't need any defrag tools for Linux filesystems however I work on quite a bit of Windows systems and defraging a filesystem in use isn't as efficient or comprehensive as taking out the drive and running it under another Windows machine. This is a pain since I have to take the hard drive out and hook it up to my main machine. I would like to have a Linux boot CD I can boot into and run a defrag program under. Are their any Linux defrag programs for fat filesystems? Also is there any problems running these on a partition that contains the Windows OS?

I would like to have a Linux boot CD I can boot into and run a defrag program under. Are their any Linux defrag programs for fat filesystems?
AFAIK none. You could run a BartPE or equiv though.

If you have sufficient HDD space, a way round this problem might be to:
1] Copy all the files/directories from the FAT32 disk to your linux disk (use tar ?)
2] Delete all the files on your FAT32 disk.
3] Copy all the files back. Then there should be no fragmentation.