One thing I've noticed of late is that there has been a pretty frequent level of deleted or invis'd comments / posts, and this can sometimes leave the users involved confused as to why a certain post or comment has been removed.
I know that it used to be policy to notify a user if their comment or post has been moderated (I made it ).
I think we need this again, otherwise people are going to start yelling censorship (and rightly so) when a post or comment gets removed and no explanation is given to those involved.
A good example of this system working is in the results thread for the Codies: posts were hidden (for a good reason, no qualms), and an explanation was given. Reasoning given was clear and everybody accepted it and moved on.
I think it's important to remember every moderator action needs to be justified and audits should be in place to make sure this is a fair and open community for everyone... or at least that's something we should work towards.