IMO instead of cluttering the emotes list or creating a second box, there should just be a locally hosted greasemonkey extension that grabs the emotes from a directory on this site. That way only the people that care about the emotes can have them available for quick use, and, because they and the script would be hosted locally, I am pretty sure that even non-Firefox browsers (which sometimes object to using userscripts to inject media from another page) would be able to utilize it just fine.
Finally and perhaps most importantly, a userscript would probably be easier to work into the forum code than if it was written straight into the php, which could easily be overwritten by an SMF update--not to mention that my dim memory of SMF backend is of a cluttered, unintuitive mess.
So uh consider that I guess.