I don't have any of the new Joe stuff, but all of my old figs are in those old school vinyl cases & one of the newer C-3PO cases from SW.
My SW figs, the new ones that is, are all in 3 different storage mediums...
1) Vintage vinyl cases, 2 ESB & 1 SW.
2) 3 of those tool drawer thingies, I've found a type that has drawers that are fairly wide, semi-deep & very long that fit most f the figs.
3) Plano tackle box, model #3730. I've got probably a dozen of those suckers & would dearly love to get more, except for the fact that there is no store that carries them anymore in my area. They still make them, as I called the company earlier this week. I may wind up ordering a case of 6 from them. They hold 15 figures, very comfortably. Most of them you just need to have in a slightly slumping pose. And the spaces are enormously deep. 3" deep, as a matter of fact. Hell, I've got Dexter Jettster & the Darktrooper in those slots & they fit nicely.
I've seen the Shimano, or whatever they're called, tackle boxed & they do look like they'd be perfect for Joes, BTW. #=$