I run a primarily paperless office, and my favorite way to read these papers is on my iPad.
I get a voyeuristic joy from seeing how intelligent people take notes. I like Walton's ideas. He's a smart chap. If you need convincing:
Since Skim does not support hyperlinks to specific pages, I had to hack together a solution myself that involved Python, AppleScript, and an application wrapper for creating a custom url handler to tell Skim what to do.