Hints of Anokata, most up to date in the manga as of chapter 898:
Taken from the DCW Wiki.
1. His(non specified, just using the masculine as defaul) phone number is the beginning few notes of Nanatsu no Ko, meaning Child of Seven (7 year old) or Seven Children.
2. Anokata is weary of Akai Shuuichi, similar to Vermouth, and believes Shuuichi alone can take down the organization
3. On the mention of Vermouth, she seems to be the bosses favorite, and cannot age. At the end of Scarlet Epilogue(I believe) Rei/Zero, says "To think you are the boss'…" Before he is stopped by the gun.
4. In an interview, Aoyama Gosho stated that Anokata has been shown already, and has been stated with full name, unfortunately, he didn't specify between, Major character, minor character, or a random suspect that has shown up in a case.
5. The Black Organization's real name gives away the boss.
6. Conan's voice actress (Aoyama's Ex-wife) knows who it is.
7. Aoyama didn't expect DC to last more than three months, so Anokata may have been hinted early on.
8. According to Miyano Akemi, the reason the operatives dress in black is because they are supposed to resemble crows.
9. Professor Agasa is confirmed not to be Anokata.
MY SPECULATION (These points correspond to the above as add ons, I originally typed them together, but then it looked very long)
1. I personally believe it's the latter, seeing how there are seven active, high ranking, black organization members (Gin, Vodka, Vermouth, Kir, Chianti, Korn, Rum)
3. At the middle of Scarlet Epilogue, Rei/Zero, says "To think you are the boss'…" Before he is stopped by the gun. This sentence can be ended with virtually anything, however, I doubt it's "Lover" because Gin and a lot of members suspects that already, so they would not be "surprised". I could be "mother" "sister" or I think any family member would be surprising. Rei obviously knows Vermouths secret to non aging. Personally, I believe that Vermouth had developed a similar drug to the APTX4869 to de-age, or stop aging, because she is of similar age to Shinichi's mom. On a slightly off track note, I believe Scotch is the source of the feud of Akai and Rei.
5. Realistically thinking, it wouldn't be his name, because imagine how awkward that'd be while recruiting. Therefore, I'm presuming it's a company or a clan, so we can narrow it down to companies and families that have shown up in DC. This company or family is very well to do, seeing how they have their own research facility, and was able to finance Miyano Atsushi, providing him with a large research space. It's very likely to be a family, because Aoyama had said "The name of the organization would give it away" For me, the leading suspicion is the Suzuki's, because they are rich, and many of their members have been named by name.
7. If anyone has owned a company or is of a large family, or only showed up once, and never reappeared again, or only reappeared a few times, that is suspicious.
8. Combined the Nanatsu no Ko thing, it makes me think that it is "Seven Children" and Anokata thinks of himself as a Mother Crow to the Seven main operatives, so this is not dismissing Anokata being a woman. The song lyrics of NnK is basically the mother crow calling her children "good" and "cute".
Anokata's motives for the organization is unclear, he had tried to have Yasuteru Domon assassinated, a man who was cracking down on crime and had plans to run as Prime Minister. It's shown that the B.O. is not a well known organized crime party, as no one on the police force knows about them. The only people who know about them are the people who specialize in espionage in their respective governments. This could be because the B.O. hides behind a legitimate corporation front, and companies that ship things are ways to smuggle in weapons, as guns are illegal in Japan (I believe). Although Anokata seems to be very fond of Vermouth, giving her a long latitude of independency, it doesn't seem Vermouth likes Anokata that much, as she has hidden Conan from Anokata, even though Vermouth had commented to herself that Conan may very well be the second Silver Bullet. Another proof of this is that Vermouth seems to be the eyes and ears of Anokata in the B.O. itself, and keeps Anokata informed. However, 3 people have successfully infiltrated the B.O. Ethan Hondou, Akai Shuuichi, and an unnamed, Scotch. It could be that Vermouth's allegiance is more to herself, and if she sees entertainment in it, she will leave it be.
Also, Haibara Ai/Miyano Shiho definitely knows something about Anokata that she isn't letting on, perhaps for Conan's safety. Because she was born into the Organization, she might know the true name.
On the topic of the Miyano's, Rei has commented once that he had met Atsushi before, making the woman who calls him 'Zero-kun' very likely to be Elena, as she's British.
This is what I gathered from what we know. Please add on!