Just a drabble that got a good reception on Tumblr, so I decided to post here.
DISCLAIMER: Don't own Sherlock, of course.
It started when John got up one morning, and found himself planting a kiss in the detective's forhead where he lay asleep, slumped on the table. He didn't register the action as odd, and Sherlock didn't question the blanket he found wrapped around his shoulders. The favour was returned when John, exhaused from a case, collapsed onto the sofa and awoke with a pillow tucked under his head and Sherlock's jacket draped over him. John smiled, appreciating the gesture, but he wasn't surprised.
The forhead-kisses continued, usually when Sherlock was at his most vunerable and in need of support - John pretended not to notice that Sherlock's emotions only took over when John was the person in danger. The little kisses were his wordless reassurance. The first time Lestrade spotted one, he raised his eyebrows, but said nothing. After a while, Sherlock returned the gesture, saving it for when John was most distressed.
The hugging was more of a spur-of-the-moment thing. A thank-god-you're-alive response that both of them needed but neither of them spoke of. They didn't need to. The cuddling was just an extention of that - an expression of affection and of relief to be back to the flat unharmed. John still shouted at Sherlock for his lack of people skills and rudeness to clients, but an apology now came in the form of snuggling up on the sofa, John's head on Sherlock's head while John watched telly and Sherlock used John's laptop. It didn't matter who was apologising.
Neither of them noticed when their relationship changed. Everybody else did.