Automatically track referenced questions
StackExchange currently has a "related questions" list that's auto-generated. However, there are frequently questions that are pointed out by users that are very closely related that never end up in that list. The only way (that I'm aware of) to link to a related question currently is to post a comment to the effect "Look here: (link)" or "related question: (link)".
I think it would be valuable (particularly for the purposes of search engine indexing, and with an eye to inclusion in the API, if it's not already too late) to add the ability for answerers to link directly to related questions, and have those links be collected together (like the auto list) but presented in a way that distinguishes them from the auto-calculated list. This way, users browsing a question can easily see and navigate to questions that other users have said are related, without having to scan all the comments to find them.
To clarify, when I say "link directly to related questions", I mean something like, in addition to the normal "answer" or "comment" options, or perhaps next to the "edit", "flag", etc. links on the question (but maybe on the answers, too), there would be a mechanism to enter links to related questions without having to embed the links in a comment.