I take some of it back. Getting the latest version of wkhtmltopdf and telling it to wait (probably longer than necessary) to process javascript, works pretty well.

    wkhtmltopdf --javascript-delay 10000 --no-stop-slow-scripts 'http://bit-player.org/deck.js/limits-to-growth-Harvard-2012-03-30/ltg-talk.html#Lotka-Volterra' slide.pdf

It's a bit slow, and a bit too hacky for me. But this tool does the best job of those I've seen.

And I've just received an email pointing me to: http://search.cpan.org/perldoc?deckjs2pdf https://github.com/potyl/perl-App-deckjs2pdf that will specifically deal with Deck.JS slides.