I'm not sure if there is a moderation system involved when you post new files or not, but it seems to me that we lack a system to report files for whatever reason. It leaves things kind of vulnerable to trolling.
With that in mind, I also think comments should have a score, like on youtube. If the comment is down-ranked so that it has a negative score, it will be hidden by default (but can be shown by clicking on a 'show' link) This way, useless or misleading comments can be hidden.
In addition, maybe there needs to be a way to report a comment all together for moderation. I see a lot of comments on files that appear to just be the person who submitted the file on an alternate account giving themselves false positive feedback.
When voting on a submitted file, you should be required to leave a comment explaining your score (which will be displayed above the comment). At the moment, file scoring is meaningless because it isn't tied to a user or any feedback! I'm not sure if its like this already, but limit voting to only people who can access a file. (i.e., while a file is premium, only premium users can vote or comment. The file author can comment as well)
The file system also needs to be changed so that script-only submissions that have become free are downloadable by non-premium users. There are tons of scripts for good files that simply haven't been recorded sitting on the portal. Even though they've passed into the "free" status, you still can't even download the script!