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"Data on a third partition? Which file system is the best go between."

NTFS is the easiest choice.
FAT will also work

If you are using Linux mostly then file permissions will be important if security is on your mind. I this case ext2 should be considered or with limited capability ext3 or ext4 can also be accessed. This will require special software and buggy drivers to access from Windows though.

I will warn against accessing the Windows Partition from Linux since this can cause Windows to throw a conniption fit.

Before making any big changes to your machine make sure to back everything up? Clonezilla and a Removable USB Drive can make this very simple.