I don't know if they still do but Sephora used to sell large decant sprays. I believe the price included filling up with the scent of your choice, though I may be wrong there.
Other than that, I don't believe anyone does. Most companies prefer to sell their products in the original packaging.
Edit: I mis-read your question. You may be able to find empty decant bottles at a number of local stores. I would start with natural products stores and hobby shops. For national retailers maybe JoAnn Fabrics, Hobby Lobby or Michaels.