Minecraft puts the data in
%AppData%, so you can just make batch files which set
%AppData% to some other location before running the game.
This is a trivial but flexible working example:
This will make that launch of Minecraft keep and look for its data (including your saves and even mods) in
%AppData%\.minecraft-supplemental\.minecraft\. (The extra level of folder structure is unnecessary but harmless, and it would be hard to eliminate it without breaking the sorts of things that the
%AppData% convention was designed to avoid breaking.)
Note that this will keep everything separate -- remembered login, achievements, saves, Minecraft version, mods -- everything. As a bonus, this not only means that you can keep different versions of Minecraft installed, you can segregate different login names into their own installs with their own saves, useful for sharing a computer with other Minecraft players.
You can make multiple versions of that batch file and change the
%SUPPLEMENT% variable to keep the copies' data separate. (Yes, it's currently set to a dumb name. Customize it to taste. I suggest
.minecraft-[username].) You can even use different Minecraft launchers by changing the
%LAUNCHER% variable, allowing different versions (or users) to use different launchers.