'The Greek Problem by candle_beck - Sometimes Watson dreamed of his life before, and in the morning he remembered it as an alien planet, dull and dry and airless. Every time he looked at Holmes, he felt like he'd just woken up from years asleep. Holmes/Watson (movieverse).
'Mistakes of our Youth' by candle_beck - As it stood: Holmes wanted to take the doctor to bed with unnerving fervour. Intricate observation led him to believe that Watson would not be entirely against such an eventuality, and further, that getting him to admit same would be the true challenge of the day. Watson had always cleaved rather closely to the ideal of a Victorian gentleman, at least in his own mind--it was a bad habit, but Holmes was fairly sure he could break him of it.. Holmes/Watson.
'Nothing Worth Having' by PR Zed - Holmes has the good sense not to complain when Watson returns to his young wife in the evenings. Mary has the good manners not to mention the occasions when her husband stays the night at Baker Street. When they meet, they are civil, if lacking in cordiality. Holmes/Mary Morstan/Watson (movieverse).
'Jack-in-the-Box' by esteefee - with spoilers for the second movie, all of our protagonists have an idea of how they might fit together and the resulting solution isn't quite what Holmes was expecting. Holmes/Mary Morstan/Watson (movieverse).
'The Case of the Stolen Doctor' by flawedamythyst - complete with artwork, a lengthy story in which Moriarty kidnaps Dr Watson and does Bad Things to him in a rich Victorian environment. Holmes/Watson (probably closer to the bookverse than the RDJ/Jude Law movie, given the artwork).