This might be a spoiler. Eventually.
I love Elementary, even though I know it's not traditional Holmes' canon. It has come to replace House in my weekly dose of socially reckless witty dialogue.
As Holmes says: Once the impossible has been eliminated, whatever's left, however improbable, must be the truth.
So I would like to put forth a theory which has not yet been proved an impossibility in the show's canon.
Holmes is his father.
The absent Holmes-Sr has been an invisible presence, hiring Joan Watson to help his son through recovery. He has invariably absented himself from face to face meetings and communicates solely via text and email.
I think Holmes-Sr is a cover which Sherlock has adopted in order to do things he finds necessary but his pride won't allow him to do himself. It allows him extra distance to manipulate those around him.
For example, Homes-Sr turned down Watson's request to extend her contract with Sherlock. Sherlock was attempting to convince her to stay, so this would seem to blow a hole in my theory.
Except I think he turned her down to see how serious she was about continuing.
If I was writing this, I would have her discover an email account which allows Sherlock to send messages that appear to be from his father. Upon confrontation, Sherlock would confess (and observe her reaction closely). Watson would be dismayed at the violation of trust. He would point out she lied to him by claiming to still be employed by his father. I could see this being a serious wedge between them which would allow for many hours of happy drama and keep their relationship from getting too comfortable.
Of course, I'm usually wrong when I see such brilliant simplicities. The series' writers rarely seem to have thought of them (or want to go in a different direction).
But it would be really cool if I was right.