Alright. Let's get this show on the road.
Personally, I just find the Agasa theory to be outrageous. But, even with all of the evidence against it, and my personal bias, we need to take into consideration the fact that there are many good advantage points the boss would have as Agasa.
1. A good watch over Shinichi and Shiho.
2. Relations in high places. Sure, he may not be rich, but his connection network is wealthed by some higher ups.
3. Without revealing who he is, he can lead Shinichi in the wrong direction, and, if necessary, right to one of the org's people since Shinichi places a lot of trust in him.
4. One last point is that, even though she betrayed the organization, Shiho is still, in a way, working on APTX 4869. He may want her alive so as to see where she can get with the drug. Then he can take her out as easily as Shinichi.
Now, for those Mouri-arty theories. I think that they are extremely interesting. The name is mentioned at the very beginning, but, if it's one of Kogoro's family members, they haven't been seen, or even fully named as far as I can tell. We can also take Vermouth's little spout on Mouri not being as innocent as he seems into consideration. But, I think she's was just thinking about Conan/Shinichi staying at the agency at that point. But it's also hard to believe that Gosho would do something so painstakingly obvious. It is just too easy of a pun to notice, and if the name of the organization would give away who is the leader AND the organization has to have power, then we would need to assume that it is named with Mouri and people would know about it. Kogoro being related to some powerful organization would be hard to hide, especially since Kogoro is quite a braggart himself.
I will not laugh at the Genta's father theory. It is quite well thought out and would certainly surprise Shiho. The guy even runs a liquor store. It shouldn't be shoved aside. It would also be cool if we could get some good information on the rest of the DB's families.
Those were just some of my favorite view points and a little of my own thoughts.
BTW, I don't think many people would be surprised if Eri was Anokata... She has that air to her that says "I can control you".
I do think the Yoko theory was pretty good as well. She appears a lot and we do not know everything she does off screen.
