I keep my spare fob under the seat, wrapped in tin foil or in an EZ-PASS shielded zip-lock bag (the bag the pass came in.) When go on trips two-up, my passenger carries it in her zippered pocket. I have spare metal keys on my keychain, and one duct-taped under the plastic in case of emergency.
When I can not lock my gear in my cases, I lock them to the bike. I have two cables, similar to this:
I run the cable through the sleeve of the jacket, and lock it to the bike with a gun-lock. Most folks who own guns have several of these kicking around:
I can also use the gun lock alone to lock my helmet to the side rack supports while it's sitting on my pillion seat.
All the cables and the gun lock are small enough to fit in the tank compartment with room to spare.