An anonymous reader writes "I've noticed that I do a lot of brainstorming on paper, and I wondered why I don't use my computer more. I realized that one of the things I like about writing on paper is the ability to arbitrarily position my text. Is there good software for OS X that lets me put the cursor anywhere I want and begin typing immediately? As for PCs, I think OneNote allows this — is there anything else? What about software that also lets me drag and drop entire blocks of text any way I want to organize them?"
I use http://www.furl.net/ which satisfies the requirement mentioned: "a good solution would have to keep copies, not just references". Furl lets you save the text of the page you have visited, as well as the link. It saves them on the furl server, so you can furl from any machine. I notice that Furl has become less popular. I don't know whether people moved to http://www.spurl.net/ instead. I think the pdf solution may be best for the long term.