I already saw in the past some presentations made with a 'cube effect' transition, similar to the 3D-multiple desktop of Compiz. I heard 'Keynotes' on Mac OSX could do that.
Is it possible to do the same on Ubuntu with PDF presentations? I tried pdfcube but it did not really kept its promises.
I think it might have helped to tell us what packages you've already tried, so we're not duplicating bad suggestions...
But perhaps you want either pdfcube or Impressive? (There was also another form of keyjnote called Accentuate, but the website for that seems to be down. I think there was some copyright issue with Apple with keyjnote.)
But word to the wise: I think such transitions are nothing but distractions to the content of your presentation, and can come off a little childish. The LaTeX beamer user's guide contains a ton of advice on how to create effective presentations, even if you're not using beamer to create these presentations, I think it's worth reading the first half of the guide.
It is now possible in LibreOffice Impress to set the transition of a presentation to "Outside turning cube". Checked on LibreOffice 3.4.5 or greater.
This requires that the 3d-transitions be installed.