Update: There are newer posts here and here.
Galley proofs of scientific articles are typically provided in the form of pdf files with ambiguous passages and editorial suggestions marked. You are then expected to add comments to the pdf indicating whether you agree to changes and/or clarifications. Well, good luck doing that.
It does appear that Acrobat Reader (9.4.x under linux, 10.1.1 under windows) does not support annotation/commenting anymore. See picture for security settings:
I fooled around with pdf2ps + ps2pdf, pdftk allow AllFeatures etc. No luck. Still no annotation in acroread.
PDFedit didn't help much. It looks like an advanced piece of software, but it offers no obvious way of making post-it type comments. The best approximation is adding text to the margins, but it's not what I set out to do.
Sadly, using wine + pdf x-change viewer (http://appdb.winehq.org/objectManager.php?sClass=application&iId=5549) is at the time of writing the best solution. You can download the free version here: http://www.tracker-software.com/product/pdf-xchange-viewer (there's also a 'pro' version)
It really is a straightforward piece of software, and does the trick, so no complaints there. However, it is very unfortunate that such a central piece of functionality is unavailable under linux.
Also, it does seem that acrobat reader is intentionally crippled -- from what I understand there is no obvious reason why commenting isn't allowed (i.e. not the fault of the authors of the pdf) other than because Adobe wants you to shill out money for their 'Pro' version (...interesting how FOSS normally doesn't market itself by adding X or Pro to the name...)