Black photo boxes with (almost) all embellishments, sorted by color. I almost always design by color so I organize almost everything by color. Some of the boxes hold more than one color, so I used the dividers that come with the photo boxes to write “YELLOW”, etc. I had some embellishments that were smaller and kept falling down and getting lost so I found some hard plastic containers at Joann's (I'm guessing they're 4x6?) and I bought one for each color. They snap closed so the items stay securely inside. LOVE this system because I had embellies everywhere and would forget about cute stuff I had. I also love this system because sometimes I'll stamp something, color it in and decide not to use it, and I can just throw it into that box.
For embellies that are multi-colored, I place in the very front, before white.
I found I seem to collect a lot of certain things (butterflies, rosettes I made, etc.) so I used part of the last box for those items, and used the photo box dividers and labeled them. For the outside of the boxes, I used kraft paper, cut to size for labels and just slipped them in, and hand-wrote contents.
And they can be stacked!