Dragon Dictation (free) From what I've heard, this is a great speech to text app.
Docs2Go ($9.99) - I'm somewhat ambivalent about this app. The iPhone version isn't as capable as the ones on other platforms.But it's still a good office app which lets you read Powerpoint and excel files, and lets you create and edit MSWord files.
Evernote (free) I've used it, and I think Evernote is the best multi-platform note taking app. It's not just that you can write or type notes; you can also attach files to a note. A monthly subscription is required for
GoodReader ($.99) This is a PDF reader that comes highly recommended. I've seen it called the best on the iPad.
Instapaper (free & $4.99) - This is my favorite way to save web pages for later reading. There are also browser plugins, so you could save a page on your alptop and read it on the iPad.
Kindle4iPad (free) - I wasn't planning to list ereader apps, but I decided to make an exception for the Kindle app. I'm sure everyone knows about it, but I want to highlight the fact that you can sync your annotations between all versions of the Kindle app (iPhone, PC, iPad) as well as the Kindle itself.
readMe ($1.99) -It supports Epub, PDF, and FB2. Actually, Epub support isn't that important if you have access to iBooks (which is not available everywhere).
What's not on this list
Stanza is the most obvious app that's not on the list. It hasn't been optimized for the iPad yet, and from the reports I've seen the user experience is marginally adequate. I'm a little surprised that Lexcycle hasn't released an updated version. I also left out apps that I'm not familiar with, as well as ones that I didn't find good reviews for.
If you like an app that's not listed here, please recommend it in the comments.