I can not be any clearer: I wholeheartedly support this. Despite hysterical objections from the usual suspects, I have seen the benefits of the backchannel firsthand. At ApacheCon last fall, Ken Coar announced during the initial keynote that there were IRC channels set up for the conference (one for each presentation room, and a main one for the conference in general). When I presented, I went so far as to put the address of the IRC channel on my first slide, to remind people where they could talk about me behind my back for the next 45 minutes. A friend in the audience forwarded me a copy of the channel transcript afterwards, and I discovered that several of the best questions came out of discussion in the backchannel.
There are people who know, and there are people who raise their hand and ask questions out loud, and they aren't necessary the same people. But if these people get together in real time, a question gets asked that otherwise wouldn't get asked, and it gets answered, and everyone benefits. Real-time is important; after the presentation ends and everyone shuffles off to the next one, it's too late.
My experience with public speaking is similar - there are people who won't ask questions in public, and people who will. A back channel provides one more way to surface some of those hidden questions. Anything that creates more conversation can't be all bad :)
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