Zim is pretty decent if you like something on the desktop and like wikis. Its strength is in quickly organizing a bunch of related ideas/notes (being a wiki) but it is much faster to use than a browser-based wiki. http://zim-wiki.org/
I tend to just scribble in Vim though, or use paper and pencil.
I tend to just scribble in Vim though, or use paper and pencil.