I've been having lots of fun with https://github.com/vimwiki/vimwiki lately! I've mixed in a bit of encryptfs to have a private directory of notes. Sometime during boot, I set it up with:

sudo mount -t ecryptfs \
  -o key=passphrase,ecryptfs_cipher=aes,ecryptfs_key_bytes=16,ecryptfs_passthrough=no,ecryptfs_enable_filename_crypto=yes,ecryptfs_fnek_sig=1a9380706fdf5bce \
  ~/docs/private/vimwiki ~/notes

I haven't done much customization yet. But one thing I'm playing with now is making it easy to post notes from VimWiki directly onto my website.