I keep a sewing machine at our beach house and I purchased a couple of boxes of Q-tips (in small plastic containers) and use the containers for machine parts. One of the boxes has my Sharpies, pens, pencils, chalk markers, etc. in it. They fit inside one of those deeper 12" scrapbooking boxes that had dividers already in it. All my miscellaneous sewing stuff is in that box - when I go to the community center to quilt with the ladies all I have to do is grab the machine, my project and that box and I have everything I need.
At home, I use all kinds of stuff to store things in but I like the containers I can see through or stand things up in the best.