I won't go into the details of how the conversation went down, as all of it has been covered extensively by others. (The following video is one example out of many.)
Suffice it to say that it was a textbook example of presuppositional apologetics, pre-planned and well-designed to make a scientist look bad, simply because the scientist tried to honestly answer questions that were by no means honest.
I think that episodes like this raise a more general question: Do I, as an atheist, want to engage in debates like that? Do I want to train strategies for "winning" those debates?
1. The issue of "winning"
To me, the issue of "winning" a debate is a rather weird concept.
Part of that weirdness seems to stem from cultural heritage. I have the impression that, in the anglo-american countries, debates are more or less seen as sportive events. There is a rich tradition of formalized debates there, that we continentals simply lack.
If you watch a "discussion" in an Austrian or German tv show, you will see 4-8 people talking past and above each other, while a rather desperate moderator tries to maintain some modicum of order.
An American "debate", on the other hand - say between Kent Hovind and Sam Harris - is a strictly formalized exchange of blows between two opponents in several rounds. The two participants are not, actually, engaging in communication with each other - they are performing a stage-play for the audience, much like the ongoing drama of professional Wrestling. And, of course, everybody goes home with the firm confidence that "their side" has won.
Call me naive, but I tend to think that discussions should be entered with an open mind and an open heart. I tend to think that discussions are an exchange of ideas that may or may not change my thinking. Ritualized exchanges of rhetorics and clever semantics designed to make the other party look like a fool simply have no part in a discussion like that.
Of course, I do not stand above the crowd. I do enjoy those shows just as much as any other dude.
On the other hand, it would be nice to see an actual honest discussion between a theist and an atheist, for once.
2. The resulting questions
The question resulting from all this is whether you, as an atheist, want to engage in public debates, recognize them as sportive events, and learn the strategies necessary for "winning". Thunderf00t clearly failed to do so. I cannot tell whether this was his conscious personal choice, or whether he conforms to the stereotype of "naive scientist" mentioned above.
And, of course, I cannot speak for all atheists.
I want to urge everyone to see that many apologists out there do engage in debate tactics. (I think there are courses out there on "how to win any debate with any atheist, every time" or so.)
On the one hand, you can see debates as a sport, and train yourself to firmly keep the ball in your opponent's field, using deception, always attacking, repeating yourself until the other party gives up, and so on. It does make you seem like a winner. And it sure is a lot of fun.
On the other hand, you might choose to always try and be as honest as you can, in any debate.
In the latter case, I also urge you to ask yourself what to do when a debate like that comes up. It is perfectly valid to simply refuse to engage in it and walk away. You can choose to have the debate, but not in front of a camera (Thunderf00t clearly didn't have those possibilities - he had something to lose!). You may choose to have the debate, at a later point, in private.
If, however, you choose to engage in (public) debates with a schooled apologist, without having been schooled in counter-apologetics yourself, you will most likely be blown to pieces in mid-air. It's not a question of intelligence or quick wit. It's simply a question of having learned the techniques and being prepared to apply them without any regard for the other person's feelings, or for logic, rationality or really anything that could step in the way of "winning". It's a battle of egos, nothing more and nothing less.
Another possibility might be that we atheists have our own schools of counter-apologetics. These would then have to be actual practical courses, instead of mere lectures on logic. You do not learn rhetorics just from a lecture - you have to train that stuff, much like boxing, until it becomes automatic.
Personally, I would like to engage in a course like that. If not anything else, it should be a whole lot of fun! I'm fairly certain that I would still like to avoid the actual debates, though, for reasons mentioned above. But it definitely can't hurt to be able to counter stupid rhetorics.