I am the biggest fan of the tracker and the issue linking (particularly as it gives you a sort of fake 'changeset' to see how a bunch of commits relate). But I do not think good commit messages should be substituted for tracker links, they should compliment each other.
I subscribe to the cvs commit list for a few reasons; one of the main reasons is that it allows me to stay in touch with bugs. I only give commits a tiny glance, 99% aren't of relevance to me and I don't have time to read them. But glancing at the the commit message keeps me up to date with bugs being fixed. If its something I am really interested in then I will go read the bug. This means that later, when a user discovers a bug in an area i've seen fly by, i'll go hunting for the bug or examine recent changes before diving straight in for a fix.
So while getting stuck deep in the tracker is the best way to get the full details of an issue I still find commit messages immensely useful. You could see them as a way to entice people like me to go read your tracker issue!
I can't remember seeing any guidelines in the docs about commit messages (other than please include a tracker issue). So perhaps it'd be good if we could come up with some suggestions.
What do you think?