I have tons of letter stickers, and rub-ons, and to keep them organized I use a standard binder with some poly-pockets. Each sheet gets its own pocket, and I group them according to style and size, separating the major sections using subject dividers. I love using this method since I can just flip through a binder to see what I have and what I would like to use.
For non-alpha stickers and rub-ons, I group them by category. If you have a lot of themed embellishments, you could designate a binder for each major theme, such a ‘baby’, or ‘summer’ or ‘wedding’, etc.
The same sort of idea would work really well with die cuts and the like, although I hear from reliable sources that using page protectors for sports cards are the way to go for that type of thing. They usually have about 9 pockets per page, and fit in a standard binder.
Remember to label the outside of the binders with the products or themes they contain for easy reference.