I'm trying to find a way to mark a USB flash device in a way that I can programmaticly test for without mounting it or changing the label. 
Are there any properties I can modify about a device that will not cause it to behave/look differently to the user?
Running Ubuntu Jaunty.
Changing the VID/PID might make your device non-usable without custom drivers. HAL isn't supposed to auto-mount your flash drives for you. 
That being said, you could always sneak something into the boot sector and/or the beginning part of the drive. There are a lot of spare bytes in there that can be used for custom purposes - both nefarious and otherwise.
How to mark a device in a way that can be retrived by HAL but does not require mounting or changing the label