I haven't had to face this situation yet but as much as I use flash drives, I probably will someday...

I would hold down one of the shift keys and insert the drive. This will keep any autorun programs that might be on the drive from starting. Then I'd scan the drive with the AV on the host PC.

I have one of the new U3 drives that comes with it's own free AV (in my case, McAfee AV on a Memorex drive.) The on board McAfee AV is manual scanning only (no real-time) but I imagine I would scan the drive with it too...