Mcgarick, if you're using a PC then why not use the Windows Backup utility? You can select the files that you want backed up and the schedule you want them backed up with. All versions of Windows 7 can back up to an external HD attached with USB, eSATA, or Firewire. (Only the Professional and Ultimate version can backup to an NAS.)
And I wouldn't micromanage how the backup software organizes your files on the backup drive. As long as it can restore them when needed, I wouldn't judge it on how it's stored.
In my opinion, simplicity of backups is an area where the Macintosh is superior. The Time Machine in Mac OS X is brilliant, useful, zero-maintenence, and utterly simple. But you have a PC so I won't won't say any more about that.
As for physical external drives, I have been extremely happy with the OWC's Mercury Elite-AL Pro. See macsales.com. I have several of them and none has had any problems. They are well-constructed and support all possible interfaces (USB, Firewire, and eSATA). They are marketed towards the Mac user but work just fine on Windows (just format them with NTFS).
Hope that helps.
Michael