I had to update a laptop BIOS when upgrading to Windows 7 using HP's own utility. Everything went okay but I made sure UAC in Vista was off and the folder holding the BIOS update files was in the root directory of C:
Whichever method you choose, make sure you have the files and method/media to revert to your current and working bios in case something goes wrong (doesn't happen that frequently but it can happen).
I've only done it once, to correct a system error on my Win7 desktop whenever the PC was put into hibernation/sleep. I used Dell's BIOS updater, very carefully following all precautionary steps before updating.
Unless the PC has a problem that can only be fixed by updating the BIOS, I leave it alone. The cost of failure is too high if it fails.
Unless the power goes off, if you're flashing the correct BIOS then you should have no issues. I killed a motherboard years ago due to flashing the wrong BIOS - I thought I downloaded the right BIOS but it was not due to me having the Pro version of the motherboard which had a different BIOS than for the standard version of the motherboard. Anytime since then when I've flashed a BIOS I've never had any issues. Having said that, it's kind of pointless to do a BIOS update unless the update fixes specific issues you are experiencing.
I used a Motherboard's Built-In BIOS Update feature for the first time recently. The flash was easy and was successful. The reason that I flashed the BIOS is that the motherboard had the first release BIOS and several later BIOS versions mentioned things like fixing stability issues and compatibility issues. I flashed the BIOS before installing the OS.
Almost every new BIOS fixes things, they just do not mention, at best they say, that it adds support for the CPU. Using outdated BIOS is no difference to outdated Windows.