hard drive upgrade

I’ve purchased a new hard drive (ATA-100) to replace my old drive. Is there a way to transfer the operating system and only certain applications to the new drive? I would like to do a virtually clean install and don’t want to do a complete ghost of the old drive (too many unused applications) to help ‘clean’ up the new disk. Or would it simply be best to reinstall everything from scratch? I’m running Windows 98.