Certainly not a show-stopper, and easily gotten around, but...
 
Do any of your programmers care to take the time to let file associations "pass through" the Command Center?
 
Viz.:  If I start Sonar on it's own, and create a MIDI file with something else and double-click it (actually, the program I use uses Process.Start(<ProcessStartInfo>), but...same thing essentially), Sonar automatically opens the file because .MID is associated with it.
 
However, if Sonar was started via the Command Center, this doesn't happen.  Double-clicking the MIDI file doesn't do anything.  Or anything I can see, anyway.  It certainly doesn't show up in Sonar.  ;)
 
This is really a minor, minor thing.  But it would be convenient.  :)