Be sure to check out the great “how-to” from Rob Dean over at WalkingOffice about using Keynote (iTunes link) and Keynote Remote (iTunes link) as a trial presentation tool. I’m not a trial attorney, but I’ve often thought that a well organized Keynote deck would be a great presentation tool if you don’t need the advanced features of something like TrialPad (iTunes link) or ExhibitView (iTunes link).
While Rob imports a presentation he created on his PC in PowerPoint, you could create the whole thing entirely on the iPad with Keynote. Note that you will need images of your exhibits rather than PDF files to use them in slides. To “convert” a PDF into an image on your iPad, simply open the PDF file on the iPad in your PDF viewer of choice (I recommend ReaddleDocs (iTunes link)), position the page you want to use as an exhibit and then press the iPad Home and Power buttons at the same time to take a screenshot. The screenshot will be added to your Photo library as a jpg. Those screenshots can then be easily added to your Keynote slides.
I also like this approach as you can highlight, circle or otherwise annotate the portion of interest in ReaddleDocs so they are highlighted in your exhibit. If you have lots of text on a page, consider taking one image without the text highlighted and a separate image with the text highlighted. Add them both to your Keynote deck as separate slides (the highlighted version as the second slide). A subtle dissolve between the slides can help focus attention on the portion of interest.
One other tip. If your courthouse has HD TVs or if you can bring along your own HDMI projector (instead of VGA), consider picking up a $99 Apple TV instead of using a Digital AV Adapter and cables. The Apple TV will allow you to project your presentation to the TV wirelessly. This may give you a bit more freedom of movement around the courtroom.
Let us know your experience using Keynote or other apps for exhibit presentation in the comments.