Big fan of Tiddlywiki for its nonlinearity. You can see how it works without signing up or downloading anything; the site is itself an instance: http://tiddlywiki.com/
I second this. For me, anything with tagging and search would work. Mine lives in Dropbox (it runs in Firefox) so it's backed up and available on all my machines. A lot of the notes and ideas in it start out on paper (e.g. written on the go, or whenever the idea strikes me) so I get the benefits of paper. But rediscovery becomes essential as the volume of notes get large. Paper is ineffective because of the lack of search capability.