The apps you want depend on what you want to do. I take alot of notes and like onenote alot. I have MobilNoter because it syncs my desktop onenote to the cloud, then back/forth from my iPad. I don't use any of the office apps, I use GoodReader to allow me to open about anything. Dropbox and File Browser allow me to get files on/off the iPad. You always want the "HD" version of an app if you can find it, it will be worth it for the enhanced resolution.
Cool Apps:
Flipboard, Netflix, Directtv, Pandora, Fandango, TheOnion, Google Earth, NASA
TV:
ABC, Discovery, PBS
News:
The Weather Channel Max+, CNN, USA Today, NY Times, Drudge Report, Engadget, Macworld, Pulse News, Local News Apps, newspapers & TV stations
Search:
Google, Bing (no i'm not kidding), Yelp, Zillow
Travel:
TripAdvisor
Social:
Facebook, Twitter, Beluga, Skype
Games:
Angry Birds (all varients),Stick Golf,Risk
Sports:
Yahoo Sportacular, ESPN ScoreCenterXL
Tools:
Alarm Clock, Ping, Speed Test, RDP, Penultimate, WebEx, VMware VIEW client, VMware vSphere Client, iBooks, Kindle