I have drastically cut down on the rust in my boxes with a simple fix I thought of from saving a cell phone. I don't have water that stays in the box, but used lures carry moisture into them. I add white rice to the container. It sucks out the water much the same way it can save a wet cell phone. I haven't had a rusted hook in my crank bait box since I started this. Just replace the rice once or twice per year.

the down side is that some will fall out when you open the box the get a new lure.... not to mention the bad jokes regarding taking lunch with me each fishing trip.

I used to have a lot of issues with rust in my boxes since I fish a lot out of a kayak and it's very hard to keep everything dry.

For the past 2 years, I have been using bull frog anti rust strips and their rust blocking spray and have had absolutely zero issues with rust. I use one strip per box and change them out annually. For the spray, empty everything out of the box and spray a couple squirts in there. Wipe it down with a paper towel in the grooves and crevices and let it dry.

http://www.tacklewarehouse.com/Bullfrog_Anti-Rust_Emitter_Strips_3/descpage-BARES.html

http://www.tacklewarehouse.com/Bullfrog_Rust_Blocker_16_oz/descpage-BFRB16.html