I face a similar problem, only that I would like to jot down notes in the margins while reading, instead of just selecting text, which means an active digitizer is needed since, AFAIK, even the best capacitive screen and stylus cannot handle this well without a lot of zooming in and out.
Not sure about the other platforms, but for Android, there are only a handful of them with an active digitizer... Lenovo's ThinkPad Tablet (10.1"), HTC's Flyer (7"), Samsung's Galaxy Note (5.3"). So it's rather easy to choose between them if the screen size is the dictating factor.
And then you need the software, all of the above use their own hacks to utilize the stylus, which is rather useless if one wants to keep the notes down the path. Android 4.0 (Ice Cream Sandwich) is supposed to have native support for stylus. Suppose the above models will be upgraded to 4.0, it would probably around mid-2012.
A standardized way to store handwritten notes into the ebooks is also needed, EPUB is still currently without one as of writing. PDF fares better.
I think it's at least two years away from having this kind of capability to (start to) mature and become affordable.
P.S. I use a Tablet PC which can do PDF annotation. However, it's too heavy, too large and not instant-on. By the time Windows 8 arrives and is adapted to 7" ARM devices (if ever, and I think 7" is the proper size for an ebook reader except for technical documents and textbooks), Android and other platforms are likely to have caught up with regard to stylus support by then.
And
I don't think I want to run the same Windows interface on the tablet and the PC. The Courier concept was probably
a better idea but well, they
killed it off.
Edit: Stumbled upon something called Jot from Adonit. Judging by the videos on YouTube, the accuracy is rather impressive (compared to other capacitive stylus). It still looks kind of weird but, if it works as advertised, I wouldn't complain about it.
Not cheap though, the normal version costs $20 and the high-end version costs $30.
Some links:
http://adonit.net/product/jot/
http://adonit.net/product/jot-pro/ (the difference between the Jot and Jot Pro seems to be an inclusion of a magnetic cling for attaching to iPad2, a rubber grip, and $10 in the price)
http://www.youtube.com/watch?v=oYp8yzkRRQA