Zite, Pulse, 1Password, Dropbox, Twitter, Facebook, iThoughtsHD, GoodReader, Evernote, Workflowy, Agenda, Toodledo, Kindle, iBooks, Instapaper, WunderMap, Chrome, and Trip Advisor.
Other than the browser and email app, I probably use Pulse, Zite, and Kindle more than the others. Reeder is also a popular news app but I've never used it.
Chrome is my default desktop browser. The Chrome sync between my desktop, iPhone and iPad is pretty sweet.
Scanner Pro is a great scanner app (I have it on my iPhone) and I understand it works very well on the iPad (I have iPad 1 without the camera so no scanning on it).