A trip to an organization store will reveal all sorts of wonderful tools to store your makeup, but to save some money, start by using what you have. For example, what about all of those free cosmetic bags that come with special offers at the makeup counter? You can keep one in your purse, one in your bathroom and then one at work so you always have your basics on hand. They're also great for keeping like items together. Put all of your eye pencils in one and your makeup brushes in another. Inexpensive pencil cases are also great for organizing both of these things.
You can also invest in some stackable drawers to keep everything in one place and eliminate clutter. The ones with the clear fronts are great so you can see what's inside. Or you can label the drawers with their contents to keep them straight. There are also boxes specifically made for organizing makeup, but a tackle box from your local hardware store will do the trick, too, because it's the same concept. This storage plan is great for college students who need to keep it mobile or people who travel a lot.
If you keep your makeup in a drawer, silverware holders have perfectly sized compartments to keep like items together. Or use a series of small baskets that all fit together like a puzzle. You can choose from clear plastic or mesh wire, or spend a little more and get some beautiful teak or wood bins.
And don't forget your makeup brushes. Synthetic brushes come and go, but ones that use natural hair are expensive and last for years if they're cared for properly. Roll up bags with compartments for each brush are optimal, but at the very least, store like brushes together and separate from others. Toothbrush holders are great for this. You want to be sure to keep liquid makeup brushes away from powder brushes to avoid any cross contamination from bacteria -- which leads us to remind you that your brushes also need to be cleaned regularly. Every three weeks or so is ideal.