I used an iPad for a show a few months back and am actually investing in my own!
One app that I think works well is "For Score." It's actually meant for musicians to upload their music and make notes and such, but you can scan full scripts into the app and add cues into the blank script. I recommend getting the pencil, so you can make lines and notes much easier because you can use pressure to make the lines harder and softer. I also like the app because I can create text, so each cue is typed, but I can also write out notes and underline and highlight.
I also upload different reports to it so I can check them off through the iPad and saving them as different dates. Word is also a great resource because you can have them automatically back up to Dropbox or Google Drive. Personally, I use Google Drive, but I have used Dropbox in the past, so I find either one to be good.