Some simple solutions I like:
- termininal velocity (TUI) lets you write and search notes stored as plain text files, recommends short notes with a filename as title. easy to work on different existing directory trees of text files.
- pass (CLI, the standard unix password manager) can be used for GPG-encrypted notes/plain text files, maybe aliasing
pass editand/or passmenu for easier access.
- rednotebook (GUI) offers word/tag clouds. stores notes in monthly text files -- with a bit of markup, though. each day offers one page for notes with formatting, including embedding images.
Wikipedia has a list of PIM and outliner applications.