Since most of the tv I watch is scrubbed squeaky clean of cigarettes these days, I was struck to see it in this episode.  I don't remember seeing cigarettes smoked in the first season, am I remembering rightly?  And there's the great opening bit in Hound where Sherlock is breaking the habit.  A nice transition.  How about the Fall?  I remember apples, and chewing gum and tea cups.... No cigarettes?

I will do more homework, and see if this observation holds water.  In the meantime i'll make a short note here, let me know what you think.

Mycroft offers Sherlock a cigarette after Sherlock identifies Irene's body from not-her-face.  She's not dead but none of us know that yet.  Sherlock smokes, low tar, "Well, you barely knew her", great stuff.

Mycroft smokes a cigarette waiting for John in front of Speedy's, waiting to tell him to tell Sherlock that Irene is in witness protection, no actually she's dead, beheaded, gone.

Hm.  When does one have a cigarette?  After a good meal.  Mid-afternoon break from work.  Oh.  And after a good ...shagging, is that the right term?  But this is Sherlock and Mycroft, no sex for you!  There is however lots of tension and intellectual stimulation, uncertainy, excitement and release... well, I thought so, anyway.   . And isn't it just like the Holmes boys?  The game with Irene is better than sex, no wonder they reach for a post-coital cigarette.

(This doesn't match my previous hypothesis that Mycroft knows Irene is alive at the end.  But I can hold multiple parallel universes in my mind to support a theory.   )