The "Z-Machine Standards Document"[1] has an appendix[2] with a very brief summary of the history of the Z-Machine; several of the other sections have tables (for the opcodes, and header formats, etc) with "V" or "Version" column showing when features were introduced.
[1] http://inform-fiction.org/zmachine/standards/z1point1/index....
[2] http://inform-fiction.org/zmachine/standards/z1point1/appd.h...
ScummVM may interest you, although I don't know if the source/developer docs are laid out to expose the VMs' evolution over time. It implements the LucasArts and Sierra VMs, supporting games from the C64/Apple II era all the way through Win32.
Interestingly, the original developer of Game Maker (back when it was still called that) had a page with history of how it developed up to about version 4.0 or something. Wonder if it's still on the archive anywhere
It'd also be interesting to see similar "release notes" for proprietary game VMs, like the runtimes of Game Maker Studio or RPG Maker—though these would probably have to be the result of reverse-engineering + wild-ass guessing.