As always, assumes a JailBroken
Kindle. Put the .bin file on the root of your Kindle's USB drive, eject & unplug, then run via the 'Update Your Kindle' link in the Settings page's Menu, not by rebooting.
Only run on a device running FW 4.0.x. (Unless I messed up, it shouldn't even run on 4.1 anyway, but, still).
Might not cleanup every crappy hack out there, bit it takes care of at least three, and at the very least should allow a clean update to 4.1. Worst case scenario, you've got a backup folder left on the rootfs and/or a now useless folder in the userstore.