Of course, the Kindle doesn't work well with textbooks so that's not saying much.
I've spent the last couple hours with NookStudy and while it has a number of usability issues, it is still the best desktop reading app on the market. It also fills a need. It's the first decent desktop reading app that supports Adobe DRM (I loaded ebooks bought elsewhere). Yes, I'm familiar with Adobe DE; I think it's crap. You should use NookStudy instead.
NookStudy is better than either the Kindle4PC or Adobe DE becuase it provides so many more annotation and search options. It also has a better looking design than the fugly one used by Adobe DE.
With NookStudy you don't just have the basic highlights, notes, and bookmarks. Instead, you have multiple types of annotations (highlight, asterisk, question) and you can do asterisks and questions in 7 different colors. You can also attach text notes as well as search Wikipedia, Google, Dictionary.com, Wolfram Alpha, and Youtube. And I just noticed that you can attach a link to the webpage you just found through the search. Attaching the link isn't easy, but it can be done.
Now I'm really impressed. I love that I can search Dictionary.com, Wolfram Alpha, and Youtube. I think this might be the killer feature for NookStudy (like indexed search was for the Kindle).
Some of the other neat features include having multiple ebooks open in tabs, and a second TOC for annotations. They're rather straightforward so I won't go into detail.
Do you know what I think? I think B&N just made themselves the leading textbook platform. Aside from the niche textbook platforms, this is the best on the market.