The short little glass jelly jars used for canning are perfect for holding perfume samples. They're short enough you can see what you're grabbing but small enough to keep the samples from falling over or getting lost.
Also, I use Target beauty boxes inside my nightstand for organizing. I'll shove the bottom of the box into the corner of the drawer then turn the lid upside down on top of it. Light items go in the top and heavier things in the bottom. Also, if you keep two of the box bottoms next to each other, you can slide the top from side to side.