Most flash drives are formatted using FAT32. This is good if you want compatibility with older operating systems. If your environment has mostly newer computers, you can consider formatting your flash drive with the exFAT file system.
Advantages
- Faster file transfers (if your thumbdrive is able)
- Support for files over 4GB
Disadvantages
- Not backwards compatible with Windows XP and Mac OS X pre-SnowLeopard
If you have more than one flash drive, you could leave one using FAT32 for the sake of compatibility.