IMHO iAnnotate is far superior. There are a couple of areas GoodReader excels (like in the automatic page fit, having two up, etc), but by and large iAnnotate does everything else more effectively. These are just a few reasons why it suits my workflow better than GoodReader: - Tabs. It speaks for itself, but having several documents open with the ability to flick between them is useful. - Sharing features. The ability to email or paste to clipboard a summary of all notes/highlights/annotations you've made is just brilliant, and makes light work of noting the most poignant areas in an academic article. - Annotation tools. They are far quicker to access than in GoodReader. If you want to highlight something in iAnnotate, you just tap the icon in the toolbar and drag it over the text (as much as you want – you can scroll through the document even with the highlight tool selected) before confirming your selection. You can set as many different colour highlighters up as you want. By contrast, in GoodReader you must tap-and-hold, drag the handles to select a continuous chunk of text, then tap highlight from the popup. If you want to change the colour of the highlight you need to tap, choose colour, confirm your choice; using multiple colours is just too time consuming. I prefer the behaviour of notes in iAnnotate too, for reviewing and revision purposes. Tapping every note in GoodReader is tiresome.