I suspect most folks organize their miniatures by category. Teos “Alphastream” Abadia explains this approach, along with recommendations for storage options. I organize by set, and then use a resource like MinisCollector to find the figures I need. But unlike the older Wizards of the Coast miniatures, the newer WizKids miniatures lack any label that reveals their set. To help organize these figures, I write the set’s initials on the bases using a white, fine-tipped Sharpie paint pen.
Bonus tips: Use a white paint pen to label your wall-wart power blocks so you know what device they power. Also, if you become a famous artist and need to sign your glossy prints, the paint pen works beautifully.