Notational Velocity (Mac only, open source) http://notational.net

It allows you to very quickly do a full text search, it saves the files as plain text, it supports external editors (I use MacVim) and it syncs with simplenote.com so I can see my notes on NV on my various macs and the simplenote app on my phone. It's very minimal and I like it a lot.

For linux users, there is nvPy: https://github.com/cpbotha/nvpy It's a pretty ugly skin, but it works.