2Screens - Presentation Expert
http://itunes.apple.com/us/app/2screens-presentation-expert/id370913954?mt=8

This is an amazing app! This app costs $4.99 but is well worth the price. Initially we investigated this app because it can use the video output to connect to a projector. After researching further, this app is all you will ever need to do a projector based presentation from the iPad.

Basic features:
First and foremost this app is a web browser. You can type in a URL and save them to bookmarks for later visits. It has a crude pointer that you can turn on/off to point to specific parts of the screen, but this is not a great feature. The user has the ability to turn the projection off in the event that the discussion leads away from the presentation and you want to "mute" it. The browser allows you to open multiple tabs and you can quickly navigate between these pages. The app provides quality documentation in both FAQ and User Guide.

Notes feature:
The app allows you to save meeting notes in a txt file that can be retrieved at any point during the presentation no matter which tool you are using. These notes only appear on the iPad and are not projected onto the screen. This is a good way to make sure that you are covering the important points of the presentation.

Whiteboard feature:
The app allows you to write in 8 colors of varying sizes. Whether you are looking at a website, a document, or using the whiteboard, you can write and annotate right on the screen. Whether the background is a solid color, a map, or a website, you are able to write directly on that item. If this isn't cool enough, the app has a built in screen capture tool that allows you to save the annotations of the screen either to the app or to your Photo Library.

Document Uploads:
You can upload documents directly from iTunes by syncing the iPad with your computer. You can also save documents directly from the web if you have browsed to them (for instance in email or Blackboard). The app will open PDFs, PPTs, and Word DOCs and then allow you to save them to the app so that you can review them at a later time. Because these documents live in the app, you can also project these files if the iPad is connected to a projector. The app allows you to access the files in your Photo Library as well or even create bookmarks to your documents for easy access.

You can also enable the speaker notes that you may have in your PPT/Keynote presentations to display while giving your talk through this app. Check out these instructions from Kathy Schrock on how to present a Keynote presentation with Speakers Notes enabled on the iPad:
http://blog.kathyschrock.net/2010/09/ipad-app-for-presenting-with-speaker.html

Like Dropbox on steroids. Sugarsync synchronizes files between different computers, so your home and work computers always match, and has an excellent iPad app that lets you access your files anywhere, edit it, and put it back online where it automatically suncs with your regular computers. Unlike Dropbox, your files stay in their original folder structure (though there is a 'Magic Folder' as well that does what Dropbox does). It's free if you need less than 2GB of storage and reasonably priced for larger sets. With Sugarsync, I can always get to any of my files through any computer, my iPad or my smartphone.