I am a researcher and use an iPad for reading and annotating research articles. One of my favourite apps is iAnnotate, which is an annotation app with tons of features and, I believe, also full text search. I keep my entire research library in iAnnotate, synced with my work computer via Dropbox.
Depending on whether you work in Windows or on a mac, you might also want to consider Papers or Sente for iPad, which have corresponding mac and/or Windows programs. I primarily use Sente, but they don't have a windows version. Both programs combine PDF management, annotation and cite while you write. Here is a pretty decent review: