One that's been recommended to me is "Papers"... I don't have it for iPad though it is on my MacBook awaiting usage this fall.
What I was told is that it is a great way to link together thoughts from all of the papers you've read ... you can link to an exact section of a paper that you got an idea from, etc. I don't have a lot of personal experience yet, but the quote I got from a postdoc in my UG lab is "I almost bought a Mac, simply so I could get the Papers app".
A pretty high recommendation, hopefully it lives up to it. Plus, its free on the AppStore.