Along with the Good advise offered already, Master Surrey...
Have surplus cash ?
We use a data drive that resides within the PC (IDE/SCSI/SATA) as an add-on. Or perhaps a USB/SCSI external drive would be best for your setup.
You can create two or more partitions on the new drive once installed/recognised by your operating system. Choose NTFS file system (best for Win XP/2000 or Vista operating systems.)
Use one drive (partition) for the busy downloads/uploads area. The larger partition could hold the files you wish to keep. (Copy)
Every now and then, a reformat of the 'download' drive will have it back in top form. The Windows physical drive and all of the installed programs/data files would be mostly unaffected using the extra drive.
Good Luck!