I've been searching for the best way to take Bible notes. It needed to have the following criteria:
- Be Digital / Search-able
- Cross Platform, Mac/PC/iPod
- Ideally something I can run on my own server and open source

What I found fits 2 out of 3, and is not bad. Evernote, www.evernote.com

Evernote for Sermon Notes

Since I don't have an iPad yet, I use my laptop during the church service.  I use www.biblegateway.com to look up scripture, and copy and past the scripture into my note in Evernote.  The title of the sermon is the title of the note, I include the date,  speaker, location and tags.  Then, just jot my notes down accordingly.  Once the sermon is published, I also link in the sermon audio to the note.