Speaking of Penny-Arcade, he also linked to the Wil Wright speach dealing with user-made content. Wil Wright was pushing a database for such content, from which the game would pull player-made species / towns / etc for his upcoming spore game.
I would *LOVE* to have such a database online to pull ship designs from for this game.
Not sure how much work this would entail, but if you could create an in-game "upload ship design" option, to a centralized database, perhaps even with a web browser side to allow for ratings of the uploaded ships, I think you could hit a user-created content goldmine. Then, of courses, give the players the option of letting the game randomly (or manually) download such ships for their enemy AI's to use.
I'm sure you've seen the GDC spore article, you know what it is I'm suggesting.