I would recommend putting in three ring binders or some other locking/unlocking mechanism to hold things such as pouches. That way you can take out the stuff that breaks (such as see-through plastic pouches).
I made a crochet case from a zip closed daytimer that I really love! Here's a link to a post about it: http://www.knittinghelp.com/forum/sh...crochet+binder
It's not all that pretty as I'm not a very good seamstress, but it's small, holds everything, is well organized, and can be zipped closed so I don't lose stuff.
I've considered using a large daytimer to make something similar for my knitting stuff. I know you want to knit something, but perhaps this layout will give you some good ideas!