When you open a PDF file, you can enlarge or shrink the image as much as you like to suit your device, highlight lines of text with different colours, create pop-up notes and associate them with a page, hand draw arrows or circle words, and so on.
In larger PDF files, like high-resolution images or maps, you can move quickly from side to side and zoom in up to 50x on a given area. In addition, you can search for text within the image itself (this is especially useful for maps).
Another interesting feature is the chance to synchronize all your files, including annotations, with any storage account you have in the cloud. That is, you can keep your Dropbox documents fully updated at all times.
GoodReader is one of the best tools around to view, manage and manipulate text in PDF files (or HTML, TXT ...). The huge amount of features, together with its power and stability, make it a really powerful workhorse of a program.