...that came to my mind while surfing on MMowned:
1. The message you get when giving rep out is something like "... you may be lucky enough to receive it in return.". New members could interpret that sentence in a way, that reptrading is common on MMowned.
If there isn't much reptrading going on around here, ignore this suggestion.
2. The thread-rating system should be improved, since in most cases the only thing that you can convey the usefulness off is the post count. I don't have the code for that, but you can decide whether doing something like this is too hard: Every time the first post in a thread gets repped, a rating of 1-10 can be given to it, which will be displayed after 10 ratings.
That way you don't have to waste time on too many crappy threads and I believe something like, that people will skip all threads, which don't have any rating, wouldn't happen. Besides, I don't know how exactly you mods are doing your work, but maybe it would also help you.