Didnt see these mentioned but quite enjoy them:
Zinio - magazine reader that does local sa stuff too. Got a sub to bicycling magazine through it.
2X remote desktop app for windows boxes
zTelnet for linux boxes and ssh
Pulse news for all the international stuff
Eyewitness news - amazing photos for current news events
Another one that is worthwhile if you have a 3G ipad is find my iphone which is free and damn useful too incase you lose the thing or leave it on a plane somewhere.
Operation Ajax, an interactive graphic novel about telling the story of the 1953 CIA-backed coup in Iran, is available free on the appstore for a limited time. I'm digging this - excellent art direction and lots of detail.
I have been using i annotate PDF this week, awesome app for marking up PDF documents with highlights, underline, bookmark, stamps you name it. I also find it very intuitive to use.
Another thing I found it does quite well is printing a web page to PDF.