-Update: The current box version is quite a bit different than the one seen here in the photos taken a year ago. Different hinge, rivets, and heavier aluminum. Also now built with better, more expensive tools! Check out current boxes at www.advgear.net-
I've been experimenting with a tool box fits behind the right pannier. This box attaches to the pannier frame on BMW panniers. I built one for myself, then a couple of friends wanted them, so they're on '09 and '11 models now.
I experimented with a different sheet metal brake and it marked the stock, so this is a 'scratch and dent' version. It'll function just fine and it's behind the pannier and mostly invisible most of the time anyway. The nice thing about this design is you can leave panniers at home, but your tools are still on the bike. I've sealed the seams, but water can get in, I put tools in a tool roll, you can jam a lot of tools in there.
You'll have to drill a small hole in the two lower pannier mount tabs, and one 1/4" hole in the box once you've held it in place and marked the box. I'll include all the fastners and bracket you need. Built with stainless steel rivets (a lot of 'em it turns out).
I changed the design a bit after riding the Continental Divide Route. There's a corner lopped off the box to avoid conflict with the rear brake bleed screw. The crud catcher arm won't hit either, but it's close.
Here's one mounted, followed by a pic of the one I've got for sale:
For this one that's marked up, $95 plus shipping in lower 48. Flat rate box would be just under $15, might be less depending on location.