Evernote works with Web, Windows, Mac, most mobile devices and mobile browsers.
Springpad works with Web, Android, iPad, iPhone.
Zim desktop works with Linux and Windows.
TiddlyWiki is a complete wiki in a single HTML file. Notable example is Garrett Lisi’s personal wiki notebook in theoretical physics.
Simplenote enables you to keep notes on the web, your mobile device, and your computer.
BasKet Note Pads is a Linux app (KDE).
Zoho Notebook enables you to create, aggregate and collaborate notes.
Nevernote is an open source clone of Evernote.