Thanks guys, I was thinking perhaps something along these lines. This is intended for motorcycle touring but the concept is the same:

http://roadgear.com/sport-touring-tool-pouch-p-46.html

But I'm open to ideas. I'll have to make a list of all the tools and parts that I'll want but definitely a couple multi-tools, spoke wrench, chain wrench, lube, spare tubes, patches, tire levers, hand wipes, along with a ziploc bag of essential spare parts. I'll need to go over the bike and trailer top to bottom to make sure I have every possible tool that I'll need.