I think mockery is perfectly fine in its place, and this place is better than many. There really is not much else one can do but mock some folks who are so lost in their way of thinking that they cannot see out of the bag -- Kleinman comes to mind.
But I think we should be realistic about parody changing minds. Comedy, jokes, are a way of binding community, much like song. The songs one likes, just like the humor one likes are one of the means of defining a group (He's a metal head, she's an emo, he likes Monty Python, they think Larry the Cable Guy is hilarious). Parody can work to change minds when it serves as a gentle reminder within a group that shares many assumptions but differs on one or two points. I don't think parody works to change minds when there is a radical difference in thought.
And there is a radical difference in thought between most of us and fundies. Science is based on the observable (not necessarily the directly observable, often only observation of consequences) and hence concerns itself with natural phenomena. Religion is based in the unobservable, the sacred, the whatever, that some believe informs and interacts with the natural world but is not itself a part of the natural world. We don't have a language to speak about that world behind the world, so we end up using our ordinary, daily language that concerns the natural world. Since our language is not able to speak properly about the "spiritual/sacred order" we use stories to convey meaning that the bare language itself cannot convey. Stories, by their nature, have a plot and a purpose. They have an end. If you've ever heard someone tell a story that seemed to have no point you probably remember how incredibly irritated you were with them. Stories must have a point. Listen to any fundie long enough and what seems to surface is that they cannot comprehend or will not accept a non-teleological viewpoint. The very language that they use to communicate their deepest concerns is always teleological, story based. We know that we are built this way, as Shermer is fond of saying, story telling apes.
There seems to be, therefore, a fundamental break between these two world views that I don't think parody can bridge. People like Shermer were able to bridge it because he was willing to see from a different perspective. He is an incredibly bright and well-read guy, not your run of the mill schmo who drinks Budweiser with his bros on Friday night and works at the auto shop.
If we want to change minds and educate, then formalized-stand-at-the-podium debates are probably not the best way to go about it. Debates are arranged so as to have winners and losers, not air ideas. If we want to engage in the free flow of ideas for the purpose of discovering and promoting truth in a Habermasian fashion, then debates won't work (at least in that public fashion of a scheduled 1 or 2 hour hashing of a few ideas). They are a side show. It is only through dialogue unfettered by communication blocks that we can move forward. Parody is a block to communication. We use it when communication breaks down and we can't move forward -- just look at what Kleinman does; he cannot argue his point and so mocks everyone around him while Adequate ends up doing the same since he's tired of repeating the same argument over and over which Kleinman won't address. But this sort of forum, in which ideas can be addressed freely and completely are, I think, the best means of bridging the gap.
Parody is fun. I used to use it frequently on another site before coming here. It is a great way of winning the hearts and minds of those already on your side, but I don't think it works to change the minds of people who think in a very different fashion.