I am just wrapping up my PhD - so I read and annotate a lot of PDFs.
A good stylus is important. There are subtle but important differences - the rubber tips have different levels of consistency which makes a whole lot of difference when you take annotations. I recommend Targus.
Goodreader is a good app. But I prefer iAnnotate. Both work, but iAnnotate feels 'smoother' when writing. With both, as far as I can recall (haven't used GoodReader for a while) you can embed annotations and highlights directly into a PDF to view on your PC.
There are countless threads on this, but eink just isn't fast and responsive enough to smoothly flip pages, look at tables, zoom in-and-out. Eye strain is a factor, but it's worth getting an iPad. I tried using SONY readers for academic PDFs, but it was just too clunky.
When it comes to rendering large PDFs, there are some differences between the two generations of iPads. The new ones have faster processors, which can save you 'seconds here and there' when handling large and complex PDFs. Whether that is worth the price difference is up to you. I would recommend buying a first gen.
Last edited by vxf; 11-14-2011 at 05:11 PM.