PhatNotes is an enhanced Pocket Notes replacement, and the Pro version supports encryption. A lot of people like PhatNotes. I am not sure I am one of them, though. I bought a license, but PhatNotes managed to lose memos on two occasions when switching between PhatNotes databases. Not sure what happened but I am wary now. But when it works it is a great hierarchical note taker.
Resco Explorer is a file manager replacement that can also encrypt files, e.g. a PocketWord document (on PPC and desktop). It will be a little inconvenient if you have to decrypt your journal file before use, and encrypt after use, each time...
TreNotes can password-protect its files. I have no idea how secure it is.