The first thing I did with my Mac Mini (Intel Solo) was to do the automatic software update, which sounds like a no brainer. However, after rebooting, the system did not come up! I re-installed everything with the DVD media, and tried again. Boom! No luck! Still no boot. This was a blow to me, and I had to sit down and think more carefully before applying all the patches.
The possible reason for the problem may come from the needed firmware update. There might be a conflict between the old firmware and the new 10.4.8 combo update.
Make sure you read the guide. It is not that long! The first update is automatically applied after rebooting and the process is very quick. However, the second one requires you to hold the power button for 10 seconds after the system shuts off. You will see the LED blink and then the update will start.
With these two firmware updates, you can now apply all the software patches with no worry and even try out the Boot Camp (it needs the latest firmware and 10.4.8) to install Windows!