I have been doing miniatures for somewhat over 25 years. Doing swaps for over 20 years. I have tons of, and I mean oodles and gobs of miniatures. They are so very hard to store and find when you need them.
At this point you are probably amazed that I can complete any miniature scene. I have tried various methods of sorting and find that sometimes that doesn't always work.
I work in two scales. 1/12 scale and 1/4 scale. My first course of action was to separate the scales. I found these neat little drawers at K-Mart. My first step was to sort between scales. This did a couple of things. It got a lot of things out of drawers, off my desk, out of shoe boxes etc.
I have 4 drawers full - the first drawer is quarter scale KITS, the 2nd drawer is quarter scale completed projects, and the last two are 1/12 scale completed projects. I rarely buy 1/12 Kits, so there is no drawer for that.
Lots of things off my desk and at least the first step has been taken.
Think about how you think of room boxes - are they by theme, by color, by period etc.
Come back to tomorrow to see the next step..