Color picker for data applies some of the principles mentioned in the article, it's more of a palette generator than a color picker put it produces very good results:

http://tristen.ca/hcl-picker/

Corel Painter has paint mixing, but I don't know how it compares to Paper's approach.

ArtRage also has a paint layering/mixing model, although I'm guessing it's using neither Kubelka-Munk nor Paper's survey-based approach.

http://www.artrage.com/artrage-studio-features.html

Krita has (or had) an interesting implementation for paint mixing that uses Kubelka-Munk: http://www.youtube.com/watch?v=lyLPZDVdQiQ