I usually put them under my bed liner. Or, in my tool box, but not with something worth stealing...
It depends on the area and where I am riding.
http://www.walmart.com/ip/12396292?...1=g&wl2=&wl3=21486607510&wl4=&wl5=pla&veh=sem
Drypak works great. I keep my phone in them and can operate the smart phone through them. Submersible. I kept my phone in my pocket at adventure island one day in one for 6 hours, submerged for up to 1hr at a time in the lazy river. No problem as long as the gasket is good.
The clamp is pretty big, so it has to be stored somewhere. I used to have one made by Aquapack that had a much smaller seal, and I would wear it under my vest infront of my chest with the strap around my neck.
You can also get the key lock like the real estate agents put on door knobs for $30 and lock it to your hitch where your chains clip like a pad lock, and it can only be removed by opening it.
You can have a key cut that doesn't have a chip in it and just spray it off with carb cleaner when you get back.
They also make gas caps with combo locks in them. Here's one example...
http://rescuecap.com/
Don't hide it in the fuel fill (unless you have a gas cap key holder) because thats the default place to put it. 1st place I'd look for a key.