I've never had any deep-seated issues when it came to flashing the BIOS on any of my systems. It's generally something I don't worry about unless it's clearly necessary, because it traditionally meant hunting down floppies that worked or figuring out whether the motherboard in question could flash from CD or USB. My motherboards of late have included handy (proprietary, but still undoubtedly handy) flashing utilities that took the whole media search out of the equation. Problem is, I can only use these handy utilities on Windows, and only one computer in the house fits that description.
All right, there is one emotionally scarring BIOS update in my past. When I built the MythTV box, the motherboard had a sensor that was confident my processor was hitting the 180 degree Celsius mark, and was subsequently shutting down. Of course, the sensor was misreading the temperature, a known issue with this motherboard, and a BIOS flash would put it right. The problem was the motherboard could only flash via floppy, and the one working floppy drive in the house was in another computer. The chassis for the MythTV box didn't have a floppy bay at all, so I ended up holding a floppy drive over the open case while the BIOS flashed.
The likelihood of these sorts of situations happening in the future for those using Linux and other UNIX-like operating systems (including Mac OS X) has just been minimized. The Coreboot project has released the 0.9.0 version of flashrom, which it says is faster than many vendor flash utilities, scriptable, and requires no physical access to the machine in question (no floppy drive, no keyboard, and no monitor? No problem!).
