When WGA detects a problem, it lets you keep running Windows, periodically popping up nag screens informing you that your Microsoft software may be counterfeit. If this happens to you, you should pursue the process that WGA presents; it may provide you with information that will help you rectify the problem.
For example, in my tests I was able to make the WGA "counterfeit" warning appear by changing the date of the system clock one month later. The Web-based WGA program was able to determine that was the problem and it suggested I reset the system date. When I did that, the WGA warnings disappeared. While most WGA detections don't resolve that easily, it can't hurt you to learn as much as you can about why WGA believes your copy of Windows or Microsoft Office may be illegitimate.
With nag screens the extent of the negative effect, WGA doesn't have much of a bite -- for now. But might that change in the future? Microsoft has said it won't "turn off" illegitimate copies of Windows. But could the software giant be interpreting that literally? The more likely preventive measure probably isn't turning off the computer. It's not hard to imagine that WGA might direct its predecessor, Windows Product Activation (WPA), to lock you out of your computer. When WPA kicks in, the computer boots to a login screen that doesn't let you use the computer until a valid activation code is entered. In Vista, this WPA screen links to an option that lets you buy a new copy of Windows, letting you use Internet Explorer for that purpose.
Microsoft has more than once alluded to the fact that it is reserving the right to enforce the installation of WGA on all computers, possibly sometime early this fall. WGA is built into Windows Vista, without any user option to remove it. It's simply not known how Vista's version of WGA will behave.
It is still possible to both remove WGA and to prevent it from attempting to reinstall after you have removed it.