I have done this once or twice and it usually works fine - you will lose any device drivers and regular applications that are not part of the OS - Acrobat Reader - Flash - Printer - etc.
Sometimes it's better to fix the real problem that causes you to think that a system rebuild is needed - you do not say why.
Check for spyware and Malware and remove them - delete unwanted applications - tidy the rgistry - defragment the disks - empty the statup list - all these can be done in an hour or two at no cost.
Good luck...
Peccavi
May 2010