I started out in a clear plastic shoebox sized box and have now graduated to a MUCH larger clear plastic box (which I am now outgrowing as well!)
Start out by separating your beads by type - little by little. Pearls, crystals, findings, etc. Also separate out tools and strnging materials. To get started, pick up a few boxes of ziploc bags. They're inexpensive, reusable and very flexible until you figure out how many containers you really need. You don't want to buy too many containers and end up being overwhelmed. The sorting process will also help you see what you have and possibly enable you to get rid of things you really don't like (is that even possible? LOL) Group the beads together in smaller ziplocs like snack bags or sandwich bags, then gather up the smaller bags into larger bags by category.
Clear plastic boxes are a lifesaver with beads. It makes it so much easier to see what you have. Tic Tac type boxes are especially helpful. You can make your own, like this:
http://www.bloglander.com/jewelrymaking/articles/tic-tac-bead-box/
I found plain ones at WalMart in the crafting section. There were 20 little boxes in one bigger plastic box with a hinged lid. I've seen similar ones at craft stores like Michaels, but they always come with beads in them. THe ones at Walmart were empty. I like these because you can group beads together but still keep colors and/or sizes separate. I have one box for swarovski bicones, one for findings, one for silver beads, etc.
http://www.beadsbydee.com/Catalog/Images/Storage/CompleteCase.jpg
Also, I absolutely recommend individual storage containers over divided boxes. If something happens and your storage box is knocked over, you have a much better chance of not ending up with a HUGE mess of mixed up beads if they're all separated into their own containers instead of in one large, divided box. I also like individual containers because it's easier to pull out the few that you're working with instead of having five or six open divided boxes in front of you, and the small containers make it easier to rearragne in different boxes as necessary.
A good tip for these small boxes when you're ordering beads that come packaged in small bags is to either peel off or cut out the label that states the size, place you bought them and item #. I buy regularly from Artbeads.com and fusionbeads.com and they label all their bags like this. I usually peel off the label and fold the sticky sides together so I can still read the info, but the sticky part is covered. Then I slide that label in the little tic tac box so I know where I got them and what they are, and the container is reusable (no peeling off lables). Another advantage to using these boxes is the fact that the larger boxes will stack on top of each other in the storage boxes.
Here's a really cool display and storage idea:
http://static.flickr.com/78/186315337_454becf1ed.jpg
Convert a magnetic spice rack (or make your own). If you have a craft room or a work station, this would make a cool display and provide you with inspiration, plus it's a handy way to store your favorite beads or larger beads. You can buy the containers from most beading stores, or you can order them from a specialty company. We used tins for our wedding favors and ordered them from here:
http://www.specialtybottle.com/index.asp?PageAction=Custom&ID=39
You can also try stack jars for working on projects. Mix and match beads and keep them together in a stack until you get to work on them.
http://www.dibeads.com/Merchant2/graphics/00000001/207A%20stackcontainerslarge.gif