Global keyboard shortcut conflicts
Integral to the operating system

In Mountain Lion, the Keyboard pane of System Preferences is not well suited to viewing all keyboard shortcuts. You can view a few at a time, but critically: 


there's no overview.


Side note: there should be feedback to Apple. 

Third party apps

The accepted answer to View All Assigned Keyboard Shortcuts draws attention to KeyCue. 

KeyCue

Whilst KeyCue does not show all keyboard shortcuts, it can present a reasonably good overview of system (and some other) shortcuts alongside application shortcuts. 

With Safari 6.1 on my Mac, for example: 



Whether KeyCue can be as effective with apps that use X11 (Inkscape, for example), and with your menu bar app: I don't know. 

Planning to avoid conflicts

With a good enough overview, you can plan properly – for not just one new shortcut, but for a range of shortcuts in the months and years ahead. Avoid conflicts before they occur. 

Observing conflicts

If a conflict does occur: Loïc Wolff's answer should be good for some but not all types. 

(A shortcut set in your unnamed menu bar app might be in conflict with something, but not appear as a conflict in System Preferences … and so on.)