The Q&A section could be improved in several ways, I am listing some ideas here.
* When clicking on an answer in the "community content" tab on the frontpage one is sent to a page displaying the answer only, with no possibility to read the question or other answers. I think the link should lead to the relevant question/answer thread and highlight/indicate which the new answer is.
* answering and commenting are closely related, and it is not always clear if one should use one or the other. should we merge the two?
* comments should be listed next to the question/answer they are referring to and not at the bottom of the page.
* Similar to the forums, we should probably have sections and subsections sorted by topics. What do you think?
Concerning answers and comments: I briefly discussed the same question with Eric recently, and he more or less convinced me, that it sometimes makes sense to be able to _comment_ on a question without being able to _answer_ it. Furthermore I also think that there are answers deserving a comment!
Concerning the placement of comments you are of course right, the current placement is solely due to (current) technical limitations.
Btw: Math overflow also has questions, answers and comments and IMO this works quite well there. It however took me some time to figure out that much of the text there actually is in comments, so maybe adding a few words of explanation somewhere (on LQP2, not Math overflow) might help :-)
I totally agree that the Q&A section can and must be improved.
Concerning answers and comments: I think it's useful to have both of them, so that not only a question but also the "quality" of an answer to a question can be discussed on a second layer (the same goes for a question). Apart from that, I think its also nice to have this "question resolved" option to see if a discussion has come to an end. But I admit that the visual aspect has to be improved (comments to a question/answer under the corresponding question/answer). However, I'm not quite sure yet how to achieve this exactly, but I guess I have some time now to figure this out :).
Concerning sections for questions: technically this should relatively straightforward with an extra field in the question for the section and views. What kind of categorization do have in mind - the taxonomy from the papers or something like "undergraduate, graduate, research-level"?
Concerning the links to answers in the "community content" section on the front page. Didn't we have a similar problem with the titles of events (pointing to the node rather than the conference hompage). How did we solve this back then?