It's not disorganized if YOU know where everything is (that's my story and I'm sticking to it).
That said, the clear plastic tubs you can get at the dollar store, in all kinds of sizes, are wonderful for things like paints, scratchbuilding supplies, "random bits of crap I know I'll need someday" and tools, among many other things. My wife turned me on to those and it's improved my modeling experience immensely.