FlipBoard, just because you have to experience Web content with it.
Dropbox for the easiest and slickest way to share files between your computer(s) and your iDevices without connecting to your computer. Free up to 2GB of files.
GoodReader for getting PDF files to your iPad.
Stanza for free books to read. Free, though you can buy books from Fictionwise and other sources.
Kindle App for best sellers. You can also read Amazon Kindle books on your PC, Android phone or, of course, your Kindle e-reader. Free reader, books will cost less than paper books. Larger library than iBooks.
Atomic Browser to replace Safari. Better tabbed interface, more windows/tabs than Safari and Ad-blocking. Worth all 99 cents.