Here is a good read on how a Version control system would store different versions of a file.

http://ericsink.com/entries/time_space_tradeoffs.html

I guess mostly it would be Deltas + Keyframe approach.

Some more reads-

https://en.wikipedia.org/wiki/Version_control
http://betterexplained.com/articles/a-visual-guide-to-version-control/