I'll vouch for swissknife, if you're trying to format fat32 for a larger storage capacity. My PVR accepts only fat32, even for a 1tb hdd. Sooo frustrating.
Otherwise go with either ntfs(windows) or ext3(linux), depending on if your application accepts it. Or if you're one of -those- types, hfs+...
Personally i use a combination of swissknife for the lightweight drive management, or Acronis Disc Director suite for all those multi-partition more complicated setups.
Also, make sure you're NOT flagging the new drive as active, or when you go to format in windows, windows will move some system files around, and you can really fudge your OS up.