My most used manipulatives are stored in little tupperware boxes that each of my students have inside of their desks!
They keep these boxes right inside of their desks. The tupperware/Gladware boxes are the kind that are "disposable" and found near the Ziploc bags. These boxes have lasted 7 years! Whenever we use a certain manipulative, my students can quickly grab it out and be ready for our lesson.
Inside of their boxes I put the most used math manipulatives that we have. It took me a few years to accumulate all of the manipulatives that I wanted in their boxes.
If you'd like the number cards, you can click here. (Tip: copy the number cards on various colors of card stock to keep them from mixing up their cards with other students at their table)