Cute question. I had a bathroom set up like the one you are mentioning. I actually purchased some beautiful glass shelves and placed them in front of the window. I just made certain I didn't store too many heavy things on the shelves which worked out well.
I also found some bins from Bed Bath and Beyond which are actually drawers. They come in extra large, large, medium and small. They have different compartments and are stackable. I would place those types of bins under my sink and this would help keep that area better organized.
If I kept my precious supples next to the toilet they would get an all too occassional yellow shower (I'm the only girl in the house with 4 guys). They don't always aim when they shoot and fire. ;-)
Currently I keep my supplies in my bedroom and schelp them to the bathroom when I need them. It's just easier that way. No one is exposed and my supplies are kept safe and hidden. My guys really don't want to see or know anything about any of that stuff. Heehee.