My son has a fun Harry Potter room, but his toys are kept in a clear plastic chest of drawers. They make his room look bad and I'm worried he'll tip it over on himself. I thought about a toy chest, but they have a tendency to smash little fingers and the toy they want is always at the bottom of the box, so the toys don't stay neat. What can I use to keep his toys neatly and safely organized while sticking with the theme?

depending on how high his bed sits off the floor, this might work
http://www.target.com/Bedroom-drws-underbed-storage-Black/dp/B001IYZCA0/qid=1242261083/ref=br_1_7/188-5978281-5666120?ie=UTF8&node=3073811&frombrowse=1&pricerange=&index=tgt-mf-mv&field-browse=3073811&rank=pmrank&rh=&page=11
This kind of reminds me of the quiditch (I know I spelled that wrong) towers, you could get fabric paint to embelish, or print out the emblems of the 4 hogwarts houses on some iron on transfers, and put a house on each panel. You would want to get 2 or 3, they are not very large
http://www.target.com/Vertical-Storage-Unit-Denim-Canvas/dp/B000H87D5A/qid=1242261083/ref=br_1_16/188-5978281-5666120?ie=UTF8&node=3073811&frombrowse=1&pricerange=&index=tgt-mf-mv&field-browse=3073811&rank=pmrank&rh=&page=11
This is multifunctional, and you can personalize it with Harry P. for a nostaligic feel
http://www.target.com/Boys%E2%80%99-Personalized-Storage-Bench-Ranger/dp/B000MVOTL8/qid=1242261314/ref=br_1_7/188-5978281-5666120?ie=UTF8&node=3073811&frombrowse=1&pricerange=&index=tgt-mf-mv&field-browse=3073811&rank=pmrank&rh=&page=15
You could also keep your eye out at thrift stores for a small wood dresser. Paint it black, then take a rectangular sponge and sponge grey paint in a brick pattern onto the dresser, it will look like the outside of hogwarts. You could print out the hogwarts house emblems and put those on the drawers as well, and use that for toy storage. Legos in one drawer, cars in another, action figures in a drawer, etc. I did this in my son's room, but with camo (his theme) and it keeps everything organized & accesible,