Like most I was intrigued by Mycroft's quote at the end of the series 3......"I'm not accustomed to outbursts of brotherly compassion. You know what happened to the other one."   

I have an interesting theory which would seem to tie up a number of lose ends from various episodes. What if Charles Magnussen is actually the 3rd Holmes brother. He was considerably older than Sherlock and so SH might not even known of his existence. Mycroft was extremely concerned about Sherlock going after Magnussen which makes me think there is more to this than meets the eye. If Magnussen was the older brother and of the same intellectual capacity but decided against Queen and Country this might explain Mycroft hiding him from SH at an early age. Magnussen becoming a media Tycoon and threatening to expose key secrets - suggests he could have information about the Royal family or the British Government, which is why Mycoft wanted him handled with kid gloves. Magnussen also had the capacity of a "mind palace" which could be a sign of the high IQ all brothers share. Mycroft's quote...."you know what happened to the other one" was after the death of Magnussen and I can only imagine a select few in the British Intelligence would know of the family link. If Magnussen was indeed the third Holmes brother then maybe Moriarty is his son. All 4 characters have high intelligence and if Magnussen was Moriarty's father this could be the reason he is taunting Sherlock and playing games with him. Mycroft could be aware that Moriarty is the nephew who with the protection of Magnussen would explain why it has to be Sherlock that brings him down otherwise Magnussen would expose secrets of the British Government and particularly Mycroft. Also this would explain how Moriarty knew all of Sherlock's secrets and his life story as Magnussen would have access to these details - Dr Watson thought Mycroft had betrayed SH, but maybe Mycroft was protecting him from certain truths and couldn't say the whole story under these circumstances. Can't wait for Series 4......!!