Hi Tom,
You might want to check in the advanced settings what folders from Exchange you are syncing, the notes folder should be an option. I have been on Touchdown for several years, we were on Exchange 2007 (been on 2010 for several months now) and I am reasonably certain that I had notes syncing with 2007. Of course I could be hallucinating too...
I'm partial to Evernote due to the platform ubiquity. You have a requirement to password your notes so that may not be an option though you can encrypt notes in Evernote.
-Ben



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