As the writer of the referenced blog post points out, there is yet no good iPad-based solution for reference management and integration with PDFs. That said, I have had supremely satisfying PDF reading and annotating experience with iAnnotate PDF [ http://www.ajidev.com/iannotate/index.html ]. Best $10 I ever spent.
A new release of its iPad software came out a few days ago and features many new enhancements including folders for organization of PDFs on the iPad.
Before getting my iPad a few weeks ago (after agonizing deliberation and internal debate), I was always a "print out, three-hole punch, put in binder, and highlight & flag passages and references" reader of PDFs. No more!
The tactile involvement of the iPad, the capacity to integrate highlights and notes across platforms (as stored in the PDF), and to manage the portability of huge stores of PDFs via the iPad, make it a true process (and life) changer for me. Much to my surprise and delight.
This likely will get even better in coming months when the iPad's overall approach to a file system and synchronization evolves, and a satisfying option is made available for reference management on the iPad. (Personally, I am a committed Zotero user, which requires the Firefox browser, so I'm not holding my breath for an easy port for my own library of references. The last time I tried Mendeley, some months back, I found it too prescriptive and restrictive in its process approach.)
One more note: I am on the Mac platform and use DEVONthink Pro 2. Auto-feeding all my annotated PDFs into DT makes researching, finding, and contextualizing vast stores of data even better and easier. AND the Devon folks have submitted to Apple an iPad version of the DT (DEVONthink to Go). How well this integrates with the desktop version remains to be seen, but the iPad's utility for researchers is great at the moment and promises to get better and better.
The iPad surely will evolve in form factor (lighter, faster; cheaper?) in the next year. Meanwhile, it's pretty sweet right now for reading and working with PDFs!
Enjoy your shiny new iPad.
PhD student, Human Development
Fielding Graduate University