Most of my documentation lives inside the source code. But the "project" source code sometimes resides in markdown/html text files near the code or on a wiki. I have mostly used moinmoin but am changing to both a custom pastebin/snippet like application as well as using evernote. Also, google docs has been a a savior in our corporate environment once or twice because many suppliers use it and it allows for great collaboration.
What i came acros yesterday was penflip.com - it may be a viable alternative. When i start a new open source project i will probably use it because of the ease of collaboration. Hope this helps!