Quickoffice Pro HD (just bought by Google) which I think is the best app for word-processing, Excel and 'PowerPoint', although Doc2 HD is very good and the most recent version supports tracked changes/review comments.
PDF and annotation
Prezi which many people find much more flexible and intuitive. What I have always done is to have my materials as PDFs, pictures, mp3s etc., and move between them rather than following the structured slide-by-slide format. I used to use overhead projectors but now use annotated PDFs using touchscreen technology on tablet computers. I have been using neu Annotate PDF which is very good, but more recently have moved over to Notability which I think is terrific. One of the good things about it is to be able to sort all the PDFs into folders. Annotation is very straightforward with a stylus. GoodReader is also very good but rather more complicated because of the number of features it has so I find it more difficult to use.
I use Scanner Pro which is a portable scanner for iPhone or iPad. You simply take a picture of a document and it turns it into a PDF file. Not the greatest quality but quite useful. I'm also going to use a Fujitsu ScanSnap document scanner as I move further towards a 'paperless workflow' (getting into the jargon here) but it hasn't arrived yet.
In the Cloud
I use mostly Dropbox but also Sugar Sync, Box and SpiderOak all offering either 2 or 5 GB of free storage - these four together give you 14GB. You can use an app like Primadesk where you can view all your data across all cloud storage in one place, which is quite useful. I also use Evernote quite a bit.
Before I had the iPad I used Zotero (Firefox add-on) but then changed to Mendeley, which is also free, and now with the iPad Mendeley is the only one unless you are prepared to buy the excellent Sente for laptop (quite expensive, $90, but the iPad app is free). Mendeley has a desktop version and an iPad version called, unfortunately, Mendeley Lite. While you can read and annotate PDF versions of journal articles in Mendeley Lite I find it a little cluncky on the iPad and tend to open them in Notability and annotate and save them there. Christopher Long of Pennsylvania State University philosophy department has some interesting things to say about all of this on his blog The Long Road.