You'll first need to decide what's most important to you: Form, function, or a combination of the two. If it doesn't matter how coordinated everything is in your storage area, you'll have more options available to you. Canvas toes, rolling bins, and plastic tubs are just some examples.
There is a vast assortment of plastic bins and totes by Rubbermaid that you can use in your closet storage area. They could be as small as containers used for food (great for craft supplies or tools), or giant tote bags for everything from patio furniture cushions or Christmas decorations.
The best thing to do with the large bins is to place them on the floor beneath the wall mounted shelves. You can then fill up the shelves themselves with bins of assorted sizes.
Labeling is one of the keys to good closet storage systems. You should clearly label each tote, bin, and tub so that you'll always know what's inside.
You should try to keep all similar items in the same place, which makes it a lot easier to see at a glance where everything is. It's easiest to use a label maker, and that way, you can just peel off the labels and change them if you ever need to in the future.
You could also write the contents on the bin with a permanent marker, or you could write it out on a piece of paper and tape it to the front/side of the bin.
Clear or translucent professional organizer bins are a great choice, since you don't have to create quite so detailed labels for them. You can see the contents at a glance, which means you can be even more organized and save yourself some time.
Rubbermaid has a great selection of these that you can use in your closet storage systems, too. Keep in mind that you can also get specialty storage for your closet, too, for gift wrap, craft items, and other hobby supplies and item.