Gruber’s current system has many flaws, including the fact that it’s arbitrarily ordered by popularity (why?) and every referrer that isn’t a permalink is going to be useless, if not tomorrow or next week then next month. For plain referrer tracking TrackBack isn’t the best, and that’s why WordPress also implements the PingBack specification, which can be thought of referrers on steroids for weblog communication, but is not widely supported at this time.
The best system I have seen so far was whatever Mark Pilgrim used when he was doing his accessibility series. It would, if I remember correctly, follow referrer links to check that the site was actually linking back, grab the context of the link (usually about a paragraph) and then find the permalink for that blog entry if one existed and link back to that. If someone were to create such a hack for WordPress I would certainly consider incorporating it with a release.