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(N.B. I don't actually have an iPad, but hope to get one once version 2 has been released.)

Out of interest do you find OmniGraffle or iMockups to be better for wire-framing website designs, as this would be one of the principle reasons for me getting the iPad?

Also, fwiw, if it is academic papers you are managing, did you try Papers from Mekentosj.com? They have a Mac desktop and universal iPhone/iPad app. I've not used the iOS versions at all but have played a little with the desktop app a long time ago (when I was still in a lab). It is built specifically for managing academic articles, so I imagine it might be better than Good Reader for that purpose but would be interested to hear first hand experience if you or anyone else has it.

TIA