I have a very nice antique desk I refinished some years back that I keep everything all organized in. One thing I will say is that the metan tins that wallets come in work quite well for shake.
i got this pretty badass box from a "box guy" at the flea market. he had all kinds with all different designs. i picked this one because of its size and shape. i only use it for smaller glass pieces like slides and spoons.
I always keep pot in mason jars because I buy way more than I can smoke in a month. As for pipes and stuff I just leave them on my desk, my bong is in between the wall and my desk. Ain't going to spend money on hiding shit.