There's at least one case I know of where OmniFocus won't quit in response to the quit command. If you have the Sync preferences window up, showing the client display (either by your own choice, or if OmniFocus is trying to alert you that you have a stale client), the quit command will do nothing more than flash the menu bar and possibly emit the system error sound. However, once you close that window, the quit command will work as expected.
Now that Omni put out that change Sep. 9 that effectively makes all of our client files go stale, there will probably be a bunch of people encountering this. Here's the snippet from the release notes:
Fixed an issue with MobileMe preference syncing and our own syncing. Now, MobileMe preference syncing will no longer copy around OmniFocus preferences for OmniFocus's syncing with iCal or other copies of OmniFocus. Also, view state and the default print profile will no longer be synced. As part of this, existing sync client entries will eventually go stale and will need to be manually removed in the Sync preferences pane. This should fix the case where the Clients sheet in Sync preferences reports the wrong computer as 'This Computer'.
So, if OmniFocus won't quit, before you try force-quitting the application, make sure you don't have a Clients window buried somewhere that is trying to bring this matter to your attention.