Marc and Evan,
Since I am still signed up for comment alerts, I see that this thread has reawakened.
Marc, if you look up at my Oct 27, 2010 comment, after scanning the Evernote agreement, it actually says (this is from memory) that it will scan your folder in order that it can heuristically suggest other things you might be interested in. No thanks.
As a sidenote, people (teachers, employers, etc) seem heck-bent on organizing their student and employee evaluations in Evernote and other things. You can see the privacy problem there I hope. Ugh.
In the meanwhile, since I have commented here, I have stopped thinking about the solution to Marc’s problem (because it is in fact my problem too, or a close variant anyway).
Long before this thread, I have thought of NAS (Networked Attached Storage). This solves so many things, first and foremost it is NOT A KLUGE.
Stick your NAS (I like the Synology 411slim, though have purchased nothing) in the DMZ of your home router, and your files are “with you” wherever you are in the world, and also not with you at TSA (and other border) checkpoints, or any other points of (il)legal seizures (not that any of us here is doing illegal stuff; you have heard that Michigan cops are datadumping smartphones at routine traffic stops?).
NASes serve all filesystems, as well as ftp, http, home video, music, surveil cams, yadda, yadda, yadda.
You can still cloak everything in Truecrypt, AND mirror your Truecrypt file nightly safely behind the firewall onto a dumb (but secure and off the Internet) external HD.
So why haven’t I done it? Meh. I’m pretty lazy really.