I was holding out on this until the 2.0 release, but I’m tired of waiting. Instapaper now supports folders!
(Note: Folders will not be supported on the iPhone app until Instapaper Pro 2.0, which is still awaiting Apple’s approval. I’m currently not planning folder support for Instapaper Free.)
Log into the Instapaper.com web interface and check out the new options on the left.
This is, by far, the most requested feature in Instapaper’s history. Enjoy!