Is there a program like xbindkeys for mac? All I want is to be able to run specific commands when a keyboard shortcut is pressed. No GUI please. I should be able to store the keymap in some file and move it around.
Another option might be quicksilver's triggers:
It's triggers are flexible and global, and can execute commands. Similar to the QuickKeys suggestions, the triggers are stored in ~/Library/Application Support/Quicksilver/Triggers.plist if you want to move them around. Quicksilver might be too much program to install just for shortcuts, but you can turn off most of it's features like indexing that you don't want.
Within the normal Aqua GUI? No. Your closest alternatives all aren't what you're looking for as they don't use a single keyboard shortcut, and they use GUIs.
If however you're using X11 (via X11.app) - you can - it can be handled by using the Customize... feature in the Application menu or by manually editing
~/Library/Preferences/org.x.X11.plist specifically the apps_menu dictionary.
The traditional way to do this on OS X is QuickKeys, and there's also Keyboard Maestro:
You'll probably find that despite having a GUI both programs would save their settings in some form of file, probably a plist that can easily be moved around.