I think that it's not Matsumoto (in the file with his daughter's marriage it shows him in the pic of in 3 years time) and I can't come up with a reason why Agasa would keep Conan and Haibara alive if he was the boss (especially if you consider that he had plenty of chance to kill Haibara when she was first introduced before anyone found out about her). Also, Agasa claims he is 52 years old (Ep 129) and has Fusae seems to back it up. Yuusaku also seems pretty unlikely because:
1) I see him as a sorta self-insert of Aoyama, an 'author', knows what's going to happen before Conan/Shinichi and is also obsessed with American/British stuff and other parellels. Of course, if you think Aoyama=Anokata...
2) Why is Haibara still alive if that's the case?
3) Yuusaku would be around his fourties, the age thing would be a big obstacle considering he wouldn't be able to wear make-up 'cause Yukiko would realise, being taught by Touichi an' all, unless she was in on it too which is unlikely. (On a side note it's quite weird how both of Touichi's students (Vermouth and Yukiko) don't look like they've aged much, shame Pandora isn't confirmed to be canon).
So, I'd say it's either someone who's had plenty of background references but has only been seen once or twice (for example: Yamamura's grandmother or that magician who I can't remember the name of...). The other option is someone like James Black (he'd have lots of connections, also I have to wonder how he so easily got a job in the FBI if he was originally from Britain. Wouldn't that count against him?) one of Kogoro's relatives (Chekhov mentioned that you don't see any of his personal history and the only reason why Aoyama would hold off so long on giving one of the most important characters a background story is if it's somehow significant to the wider plot and can only be revealed at a certain time) Youko (considering she was introduced very early on when Aoyama didn't think the series would last so long and she has lots of side mentions makes her an obvious candidate).
...there's probably more but I can't think of them at the moment. Eh, I'll just post them later...