Yes! Conan himself could be the boss of the Black Organization. I don't believe the story that Gin gave him a poison which made him shrink instead of killing him. Everybody must have been aware that this drug makes people shrink. Conan must have wanted to collected information about his Organization's enemies (Like Akai Shuichi), so he took the drug to shrink into a kid and be able to move freely without drawing attention to himself.
This is the most suspicious guy among the people in Detective Conan. I guess he wanted to test the new invention of the black organization on somebody so he used Shinichi as a subject. He must have made Gin and Vodka lure Shinichi after them, in order to force him to take the drug. He made sure that Shinichi would never figure about this by making him move to Ran's place. After a while he made Haibara comes to help him in developing this drug, and to to avoid Conan's suspicion he made her shrink, and made up the story of Miyano Akemi death.
Kogoro is also very suspicious. We all know that he didn't like Shinichi because he his deduction power was better than him. So as the boss of black organization, he ordered Gin and Vodka to kill Shinichi. Even though Kogoro has discovered later on that the poison did not killed Shinichi but made him shrink instead, he decided to leave him as he is, because he liked his new nick name, "Sleeping Kogoro", which he couldn't make without Conan. Of course, Kogoro ordered Gin and Vodka to pretend that they would kill him in episode 425 to avoid being suspected.
This famous Idol has been showing up a lot in the series with minor roles, and has been always acting innocent. But you make no mistake if you think that she is the boss. Although she seems to be good in leaving no evidence that leads to her, I think she made a mistake when she introduced Kir to Mouri Kogoro with the aim of misleading the FBI away from Kir. However, she was lucky enough that Conan didn't pay attention to her.
There are many clues that shows that Goro-chan is nothing but the boss of the black Organization. First, the fact that Eri has not showed any signs of having cats before she was given Goro-chan. Second, the fact that Goro-chan only showed up a little after Kir's case. Third, the fact that Kogoro has become a suspicious for the Black Organization. From all of this, it can be proved that the boss decided to investigate Kogoro by himself because he felt that somebody was not saying the complete truth about Kir's accident. So he first murdered Eri's former cat by giving it a poison, then he converted himself into a cat and become her new cat. His goal is to get into Kogoro's place to watch him without drawing the attention for himself. Eri's former cat did not show up because it had no interest to investigate about Kogoro. It was only Goro-chan that had interests in investigating about Kogoro.
Critical Update: (Thanks to KnightusMaximus)
After the case of Episode 309, in which Conan and Professor Agasa read Itakura's dairy, Professor Agasa continued to read further in the diary (Episodes 329-330). He found out something really interesting. The woman who was talking about "raising the dead against the stream of time", hanged up the phone after a cat cry in the background became louder. While Agasa thought that the woman hanged up because she hated cats, Conan thought that her cat was bugging her. They never thought that that woman hanged up because her boss (which is a cat) was calling her!!
Personally I don't like this theory, but I will include it here anyway. Kudo Yuusaku has hired a large number of actors to act the rule of: Black Organization, FBI and CIA. Then he asked them to play a big performance in front of Shinichi after making him shrink. The purpose of this big performance is to improve dedication skills of Shinichi. Yuusaku expects from his son to gather clues that men in black leave here and there. These clues will lead him to the only one truth, the truth that the boss of black organization is nothing but Yuusaku. All people who were killed by the black organization did not really die, they just pretended to be dead. They were just very good in acting that Conan did not notice. Yuusaku has already given Shinichi a hint that he is actually the boss of the so-called, Black Organization, but Conan did not notice. He asked Shinichi to come with him to United States in order to meet one of his friends who may be able to create an antidote to reverse the effect of APTX. This means that this friend is the real inventor of the drug, and have enough information about the drug in order to create an antidote. In fact, Professor Agasa has clearly told Shinichi that a sample of that drug is required in order to create an antidote. Unfortunately, Shinichi did not notice this.
