Onyx Boox 60. Stylus input on most formats . Definitely on PDF. Highlight, notes in the "margin", free hand notes in the notepad app. 6" only at the moment, 9.7" on its way in the new year but Superior PDF handling.
https://www.mobileread.com/forums/forumdisplay.php?f=220
http://booxusers.com/
http://www.onyx-international.com/en/
http://www.onyx-international.com/en/M_pr2.php
Irex DR 800. very similar to the Onyx, but Irex went bankrupt. If you can find a used DR 800 at a decent price its a wonderful device. But if something goes wrong they arent there to call. 8" display.
Irex also had a larger model , DR1000, which you might find used. Its PDF handling was more "complete" than the DR800(unless the last DR800 updates fixed it, Im not sure)
https://www.mobileread.com/forums/forumdisplay.php?f=99
PocketBook 603 and 903. 6" and 9.7"
Not here yet
Will have stylus input .PDF handling nearly the equal of Onyx except for one thing that might be changed when they are ready. Onyx has "selection zoom" drag a box around something on the display and that selected area is zoomed in. Dont know for certain PocketBook will have it at launch.
But PocketBook does multi column PDF reading better than Onyx and the reflow is arguably better as well.
Read the info about 602/902 it will be the same but for stylus
https://www.mobileread.com/forums/forumdisplay.php?f=206
http://pocketbook-usa.com/
Those are your choices. They all use Wacom pen tech.
The KDX is quite far behind in its PDF handling and note taking etc in comparison.
The other possibility for you is Hanvon . They make their own wacom -like stylus input and offer it on a range of devices. However they dont sell in the US. I know I've tried.
http://www.hanvon.com/en/products/ebook/index.html
They will be the first company to sell an ereader with COLOR Eink during the first part of the new year.
http://www.nytimes.com/2010/11/08/technology/08ink.html
Im sure they will offer it with stylus/pen input. But we'll know for certain in a few weeks when it is officially shown at CES the 6th of Jan.
The link below is my website. I sell both the Onyx and the PocketBook lines. The reason I chose them was for their Superior PDF handling and Onyx originally because it was the only brand to offer stylus with great PDF support outside of Irex.