In addition to addressing Thunderbolt-related issues, the updates address issues with OS X Lion's "Internet Recovery" feature on the Mac Mini, and enables it on the MacBook Pro which previously did not have this feature. Because of these enhancements, this firmware update is highly recommended for people running these systems, so they can make the best of the Internet Recovery feature, if it is ever needed.
According to the updaters, OS X 10.7 Lion or later is required to apply them, and when installed the boot ROM version on the Mac Mini will be MM51.88Z.0077.B0A.1109091226, and for the MacBook Pro it will be MBP81.88Z.0047.B1E.1109091244. These numbers can be checked by choosing "About This Mac" from the Apple menu, clicking "More Info...," clicking the "System Report..." button, and then selecting the "Hardware" section.
As with all firmware updates, the updater will download to your system and then require a restart when run. The system will need to be plugged into a reliable power source (i.e., not running on its battery), and will show a gray progress bar when rebooted for the installation. It is important that the system is not disturbed during this update, as a failed firmware update can render the system unusable.
The firmware update should be available via Software Update, but also can be downloaded from the following links:
MacBook Pro EFI Firmware Update 2.2 (4.17MB)
Mac Mini EFI Firmware Update 1.3 (4.26MB)