My favorites on the iPad (some of these are universal apps):
Downcast - A great podcast manager, lets you download podcasts directly on the deviec without needing iTunes. So far, iOS5 does NOT support this feature!
Flipboard - Makes the iPad come to life as an everchanging newspaper.
Read It Later - I prefer it to Instapaper.
Reeder - An amazing Google Reader client (although Flipboard can connect to Google Reader, it does not have any finer grain control, like reading specific feeds).
Shredder HD - My favorite chess game
GoodReader - Amazing PDF reader. I use it to read my textbooks and to manage all the files on my iPad. I have an SFTP server at home and GoodReader has a Sync folders option that lets my sync files without a hassle.
AVPlayerHD - Great video player, supports many formats.
Remote - Apple's Remote control app lets me control my foobar2000 setups on two of my PCs at home (mine and the HTPC in the living room), allowing me to browse through my media library and make any of those PCs play whatever music I want without having to touch the PCs.
AppShopper - Sends me push notifications when apps that I would like to buy have price reductions.