Here are few app that I find to be using a lot on my iPad:
Stanza - if it wasn't for Calibre, I think I'd be using iBooks.
PlainText and Evernote - used to take notes quickly, but sometimes not effectively.
But I think it's just me being a new tablet user.
"Remote App" - I use this one a lot control what's playing on iTunes.
TeamViewer - I find myself using this app a lot recently. Mostly because I'm too lazy to stand up at night and see what's happening on my PC (what's downloading, notifications, etc).
feedly - I use this one to view my Google Reader subscriptions. I'm seeing a lot of users having alternatives for this one so I might just check those out.
OPlayer HD Lite - allows me to stream media into my iPad. It's not perfect, especially with HD videos, but it still comes in handy if you don't want to convert movies for your iPad (or for quickly previewing videos).
Firefox Sync - I use this one to sync my Firefox bookmarks, but I hope Mobile Safari + iCloud could do this natively.