Ryan Cordell has recently rounded up various systems for managing and annotating PDFs. (See his original post, and the follow-up.) Those posts focused mostly on assimilating PDFs into your research, which is obviously critical.
But it’s also the case that PDFs are the format-of-choice for many administrative tasks, both on campus and off. As union president, I spend a fair amount of time commenting on PDFs related to various policies and agreements on campus. As a state employee, there’s a ton of paperwork anytime I want to do...just about anything (cf. Neal Stephenson on toilet paper policies).
One of the things I need, then, is a lightweight way to read, markup, and share PDFs with colleagues. A new favorite in this category is iAnnotate PDF, a $9.99 iPad app that puts markup and annotation tools at your fingertips.
The iPad turns out to be pretty good at this. It’s a nice-size screen, and highlighting, strikeout, and keyboard-based annotations are simple and intuitive. Here’s what the interface looks like:

It’s also easy to bookmark longer documents—sort of like Post-It notes. iAnnotate PDF also lets you draw/write freehand with your finger, which probably works better for people with thinner fingers. Moreover, you can share files easily via an in-app e-mail client. There are a whole variety of customization options.
iAnnotate 3.0 from Branchfire on Vimeo.
There are some drawbacks, most of which are related to the way iPads handle files. You can transfer files using iTunes, but I don’t want to have to sync my iPad all the time. There’s no way to access web-based PDFs through Safari—you have to use the app-based web browser to access PDFs on the web, which is a little annoying. The best way to work around this is to use long-time ProfHacker fave DropBox, which is a dream on the iPad. From DropBox, you can open a file in any application that can read it. So any PDFs saved in DropBox can be opened in iAnnotate PDF. (You can also open PDFs directly from the iPad’s Mail app.) Now, when I get PDFs to review, I save them to my DropBox folder, pick up my iPad, and there they are. It’s a little ungainly, but it works.
The other drawback is that iAnnotate doesn’t let you paste anything into a document (as opposed to an annotation). I have a digital signature saved as a .JPG, and it would simplify my life if I could paste that sucker into a PDF, rather than try to sign it freehand with my sausages fingers. Here’s what freehand signatures look like:

Obviously, this is an app for editing existing PDFs, rather than creating new ones. But the potential use cases are pretty far-reaching: you could use it to grade; to review proofs, to handle paperwork, etc.
Bottom line: if you have an iPad, and if you regularly review PDFs, then iAnnotate PDF is well worth $9.99.
Disclosure: I received a review code for iAnnotate PDF through Wired.com’s GeekDad.
[Index image by Flickr user jon_a_ross / Creative Commons licensed. Screenshots of iAnnotate PDF provided by Aji.]