Wow... quite a bit of posts...
Anyway, I vote yes for the reputations, they are better than nothing...
However... I just came up with an idea (and please read it till the end): making a sort of "comments" feature for each user, so we could leave comments (1 per user, of course) about a certain user, and qualify it as positive/neutral/negative just like in Ebay and those kind of sites. So, basically, the reputation can be a number:
Patchou (34)
Guido (0)
Batchou (-12)
I think that's more fair, plus the text comments are useful to know more about the persons' character and attitude. It's a good extension to the reputations system. Additionally, if someone is constantly flamed and doesn't really understand why, he can read his comments by other users to see how he/she can change his attitude in order not to be banned or just ignored.
So, back to the example, if next week I find out Patchou... erhm... has been logging in as another user and spamming all the forums... I can go to his profile (or click on the link in his reputation number), update my comment to "This guy started being nice, but now he's spamming all the boards" and setting my opinion on him "Negative".
Thus, Patchou's reputation would be
32 (two less), because I had previously voted him positively.
Neutral comments would be just "gentle warnings" to the users that are evidently making mistakes but maybe not in purpose.
Here again, we can make admins/mods/elites/members/newbies' comments count as 1 point, 2 points, 5 points (or whatever), depending on the group. Or just make all groups count as 1 point per comment, to make it more fear.
Bottom line: Yes, it is a complex system and yes, it seems hard to implement, but it's certainly more useful than the Post counts, The current rating or Mybb's reputation thingy. Imho, of course.
Opinions please?