OS X keyboard shortcut precedence
I think the OS X Human Interface Guidelines are the place you're looking for. They state that there are Apple-reserved shortcuts (e.g. cmd ⌘+space) and also “expected behaviours” (e.g. cmd ⌘+c) one should respect. 

While they don't explicitly state the priority, it suggests itself that the System always should have priority before the frontmost (active) and then background applications. 

From my experience, you’re on the safe side with multiple modifier keys (i.e. cmd ⌘+ctrl+shift+…).

As an aside: regarding your specific example (assigning a shortcut to open a new terminal) there's also  excellent apps for that, TotalTerminal (Terminal.app extension) and iTerm 2 (Terminal.app replacement) come to mind