In addition to the regular Powerpoint and Keynote to present documents in courtrooms, there are two major programs that are used: TrialDirector 6 and TrialSmart for Mac. These programs allow litigator to review, analyze, and present electronic legal documents with ease.
For people who prefer to use iPad, I found two apps which might be good, but I never tried either of them because they are expensive. TrialPad goes for $89.99 and Exhibit A goes for $14.99.
From the app descriptions, it seems to me that the regular iPad projection might work just as well. To organize the documents, there are lots of file management apps available: Goodreader, just PDF, ezPDF reader, Foxit PDF, Folder Plus, jsut to name a few. I personally like GoodReader and ezPDF reader. You can easily organize files into folders. Exchange files between the iPad and PC or the cloud is also a cinch.