We have encountered many of these in our Geocaching adventures.
Around the house they work great for hold small screws and parts in the shop.
Donate them to a local animal rescue. They always need pill containers to sort medications for their animals.
My father-in-law nailed the tops into a board, then filled the bottles with nails, screws, etc. He also used the same idea, but put ribbon into them for my mother-in-law. They were fabulous ideas.
Thanks for the answers, but I'm still hoping for more ideas.
I was wondering if these could be used as an art project
If you drilled a little hole in them you could push through a white strand of mini lights for garden lighting shades.
Travel sizing! If you eat take-out, you may end up with lots of small packages of salt, pepper, sugar, etc. Keep them together (sorted by type, of course), in pill bottles. There are lots of recycling/upcycling ideas you can find by Googling "Recycle Pill Bottles." Do you know the easiest way to remove those terrible labels? Pour boiling water into the bottles, let sit one minute, then peel off--easily!!
As for an art project...how about organizing art supplies instead? Or decorate them and use them as containers for small gifts.