By Private Messaging, I'm thinking of old-school BBS-style private messages.
I think gcmillwood's idea is good as-is. The only thing that wasn't addressed in his original write-up was the load added to the server per each request. I think it would be minimal, really. The notification system could be something akin to the "There is new site news" notification. The corresponding link would take the user to a new section similar to "Your Diary" that could only be viewed by the recipient. It doesn't have to be fancy and feature-filled (that is email), just something very basic and functional.
The reason I'm bringing it up now is because I'll be working on a very-similar-yet-unrelated project in a couple of weeks and could try to build them in parallel, that is, if there is enough interest and someone isn't already working on such a thing.
Thanks