They're useful for the staff to categorise the different posts. You notice you can click the thread prefix, and it will filter the view of the forum to only contain posts matching those prefixes.
In our forum, we were using them for different news categories, but we now use the Categories feature built into XenPorta.
We still use them elsewhere, but actually only in staff only forums.
I have nearly 100 prefixes set up for different forums with custom css. As much as it's not intended to function as a tagging system I use it as one and it helped me trimm bloated subforums. I also use Thread Prefix Listing
Addon that helps users to see what prefixes are avaliable and filter.