I can't imagine I would ever use thread prefixes so no from me.
Well you could definitely use them here on this website, in THIS forum. Instead of adding "[SUGGESTION]" and "[Already Exists]", etc, you could just apply a prefix.
I also think everyone begins mixing up other features. Prefix is a prefix, something to add before a thread title. Suffix is a suffix(although no one mentioned that), something to add after a thread title. Labels are labels, something you can label your threads with, kind of like a category. For instance you could have a label called "Sci-Fi" which would be added as label to every thread that you want to be able to group as sci-fi. Tags are tags, words that describe the individual thread. For instance you could have tags like "Star", "Trek", "Captain", "Janeway", "Klingons", "Starship", "Voyager", "Enterprise", "Future", "Space", "DVD", etc. Aswell as a label "Sci-Fi". And even a prefix of "Selling:" since he's obviously trying to sell a Star Trek Voyager DVD box
You could make use of all systems on the same forum but I think it would get very complicated and confusing. And I'm aware that everyone would probably define Prefix, Label and Tag differently. However, this thread was about prefixes so let's discuss that!
I'm all for prefixes, as said it could be used quite efficiently on this forum and I'd have several uses for it myself.