For my embroidery threads (FUFU now Floriana) I organize them by their color chart on my pegboards. I also printed the color # below each hook so I know where they go back. My quilting threads (mostly Connecting Threads) are organized by like colors on their pegboards, the larger spools are on a separate pegboard. My Aurifil and odd brands are in a drawer near the frame. My serger threads are above my sergers (2) and my regular threads are organized by colors on pegboards above the 2 sewing machines. All have 36 x 36 tee towels over them to keep the dust off. I keep the filled bobbins on the peg hook under the spool they go with.
For my quilting bobbins I'll use up the leftover threads on the bobbins for when I baste the quilt sandwich so I can eventually have my bobbin back. Mostly I use the bobbins with little thread left on them for this procedure.