When I'm at school, I use Goodreader to read, highlight and mark-up PDF files. I've taken PowerPoint slides, saved them as PDFs and then used them in class to go along with the teacher's lecture, highlighting and annotating as needed. Goodreader also allows you to save the highlighted PDFs in such a way that any other PDF reader can read/view the annotations.
I also like its folder organization. I can put documents into sub-folders so that I can go right to a certain class's notes.
Plus, you can download anything into the app, even stuff it can't open natively (e.g. epub files). Then, I can choose the "Open In..." function to open the item Goodreader can't. But, the item can still stay in a nice, neat folder within Goodreader.
Organization. That's what I like most about Goodreader.
Marilyn
P.S. Essentially, what Tim said! He just types faster than I. Oh, and Tim, hope you don't mind, but I've "stolen" your Swiss Army knife analogy for use elsewhere. It's a perfect description of Goodreader...