Macjournal, how I love you.
For the last five years I’ve used Macjournal in one edition or the other (professional, standard, and the original free edition) from Mariner Software. I just dropped $34 on the new version, primarily because of it’s auto-encryption feature.

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It’s become my repository for all things of interest at work, meetings, and conferences. When I left my last job, I was able to hand them a single set of files containing over three years of notes (the export feature can format for HTML, Livejournal, a number of blogging sites, an text). I loathe paper. You can’t search it, copy it, or easily distribute data that has been imprinted on pressed vegetation, although it’s role as a prevailing information technology for centuries has proven it’s worthiness.
I’ve experimented with EverNote, but it just can’t do what MacJournal can do. One of my favorite features is the cut-and-paste of web sites (complete with graphics and all layout). If you read Safari (O’Reilly’s online library) like I do, this lets you cut and paste entire pages of books and hang onto them.
The key feature in Macjournal 5 for me is automatic encryption and locking of journals. You can set specific journal folders to encrypt and lock after a period of inactivity, which makes for an ideal password and sensitive information store.