Oh, I have so much makeup it's hard to keep my stuff all organized. One thing I do have is a desktop organizer, like a secretary would use, for on top of my bathroom counter:
The one I have is larger, with more compartments,. In it, I keep all of my tubed lip glosses, eye pencils, lip pencils, all of my brushes, roller perfumes, and sample vial perfumes. There are also a couple of other odd compartments where I store my eye primers, concealer, and some samples. It has been a life saver for me. Especially for the brushes and liners... where it is difficult to grab the one you want when it is in a drawer, mixed around with other things.
The only eye shadows I use are loose powder mineral shadows, and no matter who I buy them from, I transfer them into small 3 gr. sifter jars, where I write the shade name on the bottom. Those go into my makeup drawer in my vanity, divided into little divider boxes also from the office supply section of a department store. Easy to organize, find what I'm looking for and what when something is missing!!
I'm about due for a purging of my two drawers.... some things just aren't getting used, are out of date, not my shade, etc. No sense of it lingering if I am not going to use it!! (Plus the longer it sits, the more apt it is to go bad!)