All your thoughts in one place: Evernote
I have been using Evernote for over a month now and I have to say this is really one of the best note taking apps out there. This is not just because of the app but the fantastic integration with mobile devices, multiplatform, clipping web pages and much, much more.
about: Evernote allows you to easily capture information in any environment using whatever device or platform you find most convenient, and makes this information accessible and searchable at anytime, from anywhere.
Evernote is available for Mac and Windows, has a web app (automatically synced with your desktop), mobile app and iPhone web app. Taking your notes could not be easier, from using your desktop app to taking pictures with your phone and mailing the pics to the web app that is synced instantly with your desktop.
Evernote is curently in beta stage so you will need invites if you would like to try itout. I have 17 invites available so if you want to have a go, leave a comment and I will send you an invite.
The site has very good tutorials/ideas on how you can use Evernote. You can also check out rohdesign's public notebook SXSW Sketchnotes.