I've tried a number of software and web based apps for electronic note taking, and always have ended up going back to analog. For the past few weeks, though, I've been making great use of EverNote, a free Windows note taking app. You can easily create a new note from anywhere in Windows by typing CTRL-ALT-N or paste directly into a new note by pressing CTRL-ALT-V. Notes can be tagged with categories and it also has "auto categories" for quick searching. Evernote also has a keyword based search tool which works fairly well. There is a premium version that supports digital "ink" via TabletPC as well.