I have a MacBook Pro and I am planning to do a fresh install of Mountain Lion over my existing Lion partition. I have Windows x64 installed on another partition (I installed it using BootCamp). My question is whether I have to remove BootCamp windows partition before installing Mountain Lion? Or may I just install a fresh copy without disturbing Windows partition?
It shouldn't affect your BootCamp partition, I upgraded to Lion and ML on two macs without any issues.
If you want a completely clean install and you're booting from a USB drive with the ML installer, then run the disk utility to wipe the OSX partition, and choose that as the destination for installation afterwards, it still won't touch your Windows partition.