...The most useful merchant ship killer other than a U-boat is a cheap and cheerful commerce raider based on a converted merchantman, able to clandestinely mine the approaches to a major port, provide support to U-boats and fire guns up to 150 mm calibre at targets of opportunity. I refer, of course, to the HSK (HandelsSchiff Kreutzer) auxiliary cruisers, some of which had an Arado seaplane as a spotting aircraft.
May I introduce you to
http://en.wikipedia.org/wiki/German_auxiliary_cruiser_Orion which did rather well minelaying off New Zealand. 62,915 registered tonnes sunk.
And Thor
http://en.wikipedia.org/wiki/German_auxiliary_cruiser_Thor 96,547 registered tonnes sunk or captured.
The famous Kormoran actually sank a Light Cruiser (HMAS Sydney) so although it was lost in the action, it was strong enough to do its job.
I have to say that the nine HSK were remarkably effective, in aggregate sinking over 140 ships (over 700,000 tonnes of shipping). I have considered the effects of a deliberate prewar policy to build and send a fairly large number out as covert sub depot ships. They can trade commercially until it's time to break out the crated guns and assemble a light seaplane. Not as satisfactory as a converted Q-ship, but a bloody pest for the allied navies and useful to the U-boat commanders.
So there - in terms of tonnage sunk - is your most effective anti-commerce weapon. Not very glamorous, but the original naval pain in the bum.