Wood is probably the easiest stuff to seal up and work with for something like this. If you don't need it to last a super long time, (or you are willing to soak it in a wood sealant or lacquer it or something) you can use thin masonite for the side panels, and plain old white pine or whatever is handy for the "frame" that gets fixed to your bike frame tubing.
If I were to make a really quickie triangle frame for packs of something RC-LiPo-sized or smaller, I'd use 1x3's fastened (screwed and glued) into a triangle just smaller enough than my bike's triangle to fit snugly inside it, with recesses (countersunk screwholes) for the water bottle mounts.
Then I'd use fender washers and countersinkable screws (something with a thin head, at least) to secure the frame to the bottle mounts on at least one tube (and two tubes if you have two bottle mounts, like some bikes have one on top of the downtube and one on the front of the seattube).
Then I'd use hose clamps thru small slits (sealed with silicone later) to secure the top of this to the toptube.
Then I'd screw one masonite side panel to one side of the wood frame, with a permanent sealant between them (wood glue, most likely).
Then I'd make a gasket (old mousepads or thin exercise mats may work if they are dense closed-cell foam) for the other side of the frame and glue it on. Wait for that glue to dry, so it doesn't get all over stuff, or sponged into the foam and cover on the next step.

You may want to make a notch in the bottommost corner of the gasket for wiring to exit/enter, just wide enough to allow the main wiring thickness to pass thru (the edges of wiring will compress the foam a little and help make a seal).
Then install batteries and wiring, and fill any empty space with blocks of leftover wood, and the least-compressible foam I could find (liek the rest of what you used for hte gasket, for instance), and run your main power (and/or charging) wires out the notch in the bottommost corner of the gasket.
Then screw the other masonite cover down over this.
Paint, if desired, and wait for it to dry before you ride it.
There's also lots of other ideas in this thread:
http://endless-sphere.com/forums/viewtopic.php?f=3&t=12847
and here's a search on various battery case threads for a list of others:
http://www.endless-sphere.com/forums/search.php?keywords=battery+case&terms=all&author=&sc=1&sf=titleonly&sk=t&sd=d&sr=topics&st=0&ch=300&t=0&submit=Search