I'm curious to know what other stitchers do with any leftovers. I tend to use mini kits and such like to keep my fingers going in between bigger projects but invariably end up with odds and ends left over. A lot of them are clearly marked as a proprietary thread such as DMC or Anchor - do you wind them onto bobbins of the same code that you already hold? I thought about making up a little book of punched cards with the numbered threads stored in but knowing me it's the last place I'll go to if I need a length of whatever.
I put all my leftover threads in a Ort bag I keep next to my sewing box and when it is full use the threads as stuffing in my "small" makes, like Biscornu's, humbugs or other small decorations.
If there is enough thread left from a kit to make a good start, I usually donate it to a local charity shop, or ask the gals on here if they would like it as I don't usually do the same design twice.
Your idea of winding them onto bobbins is a good one, especially if you love those smaller designs as in between projects, but most of my designs are usually Dimensions or Bothy Threads, which one has it's own numbering system and the other don't give the Madeira numbers, so it seems pointless to keep them for other projects.
I have tried to keep them on bobbins myself, but then I totally forget I have them anyway!
I add them to my stash if they are long enough odd tiny bits go into a plastic bag to use as stuffing.
My threads are on those little cards in the thread boxes but I only use ever other cube in the box for the bobbin cards and put the ends into the empty cube space next to the cube with the card of that colour on it.
I came across an idea in a book once, one called Alphabets and Samplers where you could take a letter, back stitch the letter onto aida, evenweave, etc as a guide and then fill in the background randomly with small bits of left over thread. I find it useful to use up my left over bits and threads which have strayed from marked bobbins.