I've used both EverNote and OneBNote, but am currently using OneNote.
Comparisons: in this regard - encryption - EverNote seems to win. (Assuming the crypto is done properly)
Lifehacker Faceoff: OneNote vs. Evernote: "In OneNote, you can encrypt entire notebook sections, but that's only for the premium (paid) Microsoft Office versions. In Evernote, select text and right-click to encrypt it."
'via Blog this'