I've found my iPad to be pretty good at dealing with academic PDFs, but there are still some difficulties that make it annoying. I started taking it to my discussion classes instead of printing the day's paper out, and it worked great. The PDF is reproduced exactly as it prints, and you can quickly scroll from one page to another, search, and zoom in on interesting bits. The ACM two-column format works well with the iPad's PDF reader and iBooks.

Later in the year the professor showed up with an iPad as well. :)

(There are apps to organize and cite papers with, like Mendeley, that help somewhat, but I haven't found a great one yet.)