I feel like I could use transparent, seamless folder compression.
One way to achieve this, I think, is to compress normally, and mount an archive with Nautillus. AFAIK. you can run programs from the mountpoint at a performance hit. My only worry is that the mountpoint won't match the original file path that folder existed at.
With the NTFS "Compress this folder to save space" feature, all programs and files can do all file operations though the mount. Including software that really cares were things are, like linked libraries and hundreds of application assets.
Ideas? I Currently use ext4 like a nobody but am open to play with more exotic file systems.