I was quite pleased that it turned out there wasn't a super-key after all, because really: that idea was preposterous. Apart from anything else it would require that, at some level, all the computers in the world have the same instruction set, and they don't. Moriarity did point out during the denouement that it was preposterous, which leaves the question: why was Holmes willing to believe it in the first place? He does answer the question as to how he broke into those places[1] and nobbled the jury, which basically comes down to: because he's Moriarity. He can arrange any crime he likes: that's his whole purpose. Just like Mycroft can bring in Moriarity on a whim (despite the latter's vast criminal powers), because he's Mycroft. And Holmes, in the end, can make his extraordinary deductions because he's Holmes, and not because, when you look at it closely, the conclusion actually follows from the evidence.
The show's writers always had a bit of a problem with the 'twist' at the end, since it's one of the most famous fake deaths in fiction, so there wasn't ever going to be any element of surprise. But they don't help themselves that only two episodes ago, Adler faked her own death twice, and the first time she faked it sufficiently convincingly to fool Holmes, so being able to fake your death so as to fool Watson doesn't seem like much of an achievement in comparison. There's been a lot of chatter online as to how he did, but I can't really bring myself to care. Of course he was able to do it, because he's Holmes. The exact method barely seems to matter.
[1] Incidentally, breaking into the Tower of London is the easy bit. The difficult bit would be getting away with the Jewels, so Moriarity rather failed to impress.