He doesn't think about John Watson nearly as much as John Watson thinks about him. This is no surprise. Sherlock Holmes' mind is spent on solving mysteries surrounding crimes whereas John Watson mind is spent trying to solve the mystery that is Sherlock Holmes. He never considered John much of a mystery. He could easily deduce nearly anybody's habits within a matter of seconds. The first moment he met John he could tell what type of razor he used, his inability to sleep, the pain in his leg was psychosomatic, his income and the list went on. Before any of that, the very first conclusion he drew was that John Watson used to be a soldier.
It was the posture that gave it away. He stood straight and tall, eyes focused on Sherlock Holmes. A good soldier standing at attention. Watson did this almost any time he stood still. More so, Sherlock was convinced that he could walk in at any moment of John's life and no matter what the first thing that would come to mind was John Watson used to be a soldier. He ate, walked and gave commands like a soldier. Though Watson is left-handed, Sherlock observed that he could easily hold a gun in either hand. When he was captured, John blinked out a distress signal that soldiers were trained to do.
You could take the soldier out of the war, but you could not remove the war from John Watson. Many nights John could be heard waking up from a nightmare. On the nights John didn't sleep, Sherlock had seen him pacing the living room keeping an eye on the doors and windows. A good soldier keeping guard. Sherlock showed him a new life that gave Watson the danger and adrenaline rush of war without leaving his homestead. The nightmares tapered down some and John slept slightly better. Then one night it happened.
Sherlock walked in and found him asleep on the armchair. His arms were spread out, his legs were crossed and head lolled back. For the first time, John Watson did not look like a soldier. This troubled the detective consultant more than it should have. Sherlock Holmes had never considered his flat mate a mystery. Yet for some reason, looking at the sleeping man, his mind conjured a question. He was curious to know who John Watson was before he was a soldier. That is what bothered him. He had never taken an interest in anybody that was deeper than what he could deduce. His mind, which was more interested in the dead than the living, wanted to know more about the man he shared a home with. Holmes decided two things that minute. He chose not to ask his colleague about his life in the past, that mystery would unravel itself in time. He also decided that John was beginning to mean more to him than he would readily admit.
A/N: Thought of this when I realized that Martin Freeman seems to keep the posture of a soldier almost all the time.