Compressing the folders using windows' drive compression might help.
If you could transition to a linux machine running eclipse, the reiser filesystem was made for this type of file storage. XFS and ext4 would also perform well in this situation. Both Reiserfs and XFS are able to pack files together to eliminate free space waste, reiserfs achieves almost zip levels of space savings in certain situations. Packing files like that also makes data recovery nearly useless if the hard drive is formatted or the partition table destroyed.
Reiser4 is even better, it has gzip compression built in as an optional function of the file system.
If you could transition to a linux machine running eclipse, the reiser filesystem was made for this type of file storage. XFS and ext4 would also perform well in this situation. Both Reiserfs and XFS are able to pack files together to eliminate free space waste, reiserfs achieves almost zip levels of space savings in certain situations. Packing files like that also makes data recovery nearly useless if the hard drive is formatted or the partition table destroyed.
Reiser4 is even better, it has gzip compression built in as an optional function of the file system.