Actually Explorer manually reloads environment variables when you change them, and nothing else is affected.

That's a neat trick, thanks for pointing me out. I've always wondered how Windows could have accomplished that. It's a shame that Linux doesn't have such an equivalent. If we are to do the same thing in Linux, a login shell (bash or zsh or even GNOME) would be the right place to implement?

There's a recent post from Raymond Chen about this, actually: http://blogs.msdn.com/b/oldnewthing/archive/2015/09/15/10641...

The same on both system. You have to stop and start cmd.exe/etc again. In older Windows versions you had to reboot/re-login.

source ~/.bashrc

And this will change it for programs I launch by clicking on the launcher menu?

You could have the launcher source your .profile/.env/whatever on every app launch. Count it as a bug in your launcher ;)