Normally, if you have had some tough-to-remove malware on your system, then they would go away with a format and reinstall of Windows. But, if you get rootkit infection, then that can be hard to remove. I don't know how the rootkit survives the formatting, but I have read that even after a format, the infection can be there... so in case of rootkit infection, you can choose to wipe the disk. I don't think its required in cases of other kinds of infection. I am not an expert however, and someone with more knowledge than me, will be able to tell you better.
Yes, there are BIOS virus too, and these won't go away with a reformat, and reinstall. For these, I think you can remove them with a antivirus rescue CD, which has got such capability to remove boot virus. I don't know names of any such CD which might have this feature though.
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Anupam
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