Autolinks and greasemonkey
Looks like Mark Pilgrim has "come out of retirement":http://diveintomark.org/projects/butler/ with some google enhancing GreaseMonkey scripts. I think the whole idea behind GreaseMonkey is that users are in control of their content. If I recall, it was originally used to fix usability issues in websites, very similar to user stylesheets.
Recently, I did install and give the new toolbar a test drive. It wasn't long before it was uninstalled, but I noticed one thing: I never clicked those autolinks. The Autolink button provides a dropdown of the autolinked elements which I found more handy than digging through the page for it.
Why not skip the whole autolinking business, route around the whole controversy, and just provide a nice list of found addresses, ISBNs, Phone Numbers, etc?