06/14/2009 Update: It now works with the just-released Safari 4, too.
Someone wrote to tell me that MiddleClickClose was no longer working after upgrading to Safari 3.1.1. I hadn’t yet installed the latest version, so this was news to me. I just upgraded, but MCC still worked for me. I’m not sure what the user’s problem was. Maybe he upgraded from Safari 3.0 to 3.1.1, skipping 3.1, which I can see how that would have broken it for him.
I did change the MaxBundleVersion in Info.plist to 5525.18, which is the current version of Safari, so if you’re having problems, install the copy linked below. Or edit the Info.plist file in MiddleClickClose.bundle/Contents yourself.