I have toyed with NoteCase as an outline based note app. KeepNote may be a bit more capable but NoteCase allows you to encrypt the file. It also has versions that run on Linux, Windows, and Mac. The downside is that the author has moved on to a commercial version of the program.

Still, the note app I use on a regular basis in Xournal. The key is that I can take notes with my stylus, including the ability to import a PDF file, mark it up with my stylus, and export a new PDF file. The downside is that each note is a separate file (although it can be multiple pages). It also doesn't support encryption.