I think that either Notch or a modder should come up with a boat house option/mod. you could craft a control block, which could just be a boat encased in a material in the crafting area, and you place the control block wherever on the boat house to move it! one week to vote
There's already a mod like this, it's a work in progress though. It does pretty much what you describe, taking a structure and making it into a zeppelin. Not sure if it works for a water-bound ship though. There's a spotlight from the Yogscast guys .
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