Mac OS X Yosemite global keybinding management

Question

I have recently moved from linux to Yosemite and by far the most annoying thing about Mac OS X are the severe limitations in window manager configuration. Being an emacs user my fingers automatically press Cmd+M to "go to the beginning of what I am writing". But for firefox and iTerm that minimizes the window. The main question is, how do I pass this specific binding to the application?

To generalize, what is the lowest level that I can configure keybindings? Ideally I would have all global keybindings managed by Slate (or a similar application).