I’ll keep an ongoing list of possible WhoLock crossovers below. You guys are welcome to use them for fanfics, of you feel so inclined, just please send me the link so I can read it!
Sherlock isn’t actually a human. He’s a Timelord, and Molly is his companion. He stored his Timelord self inside his pocket watch, which Mycroft keeps safe for him. (See a Study In Pink.) only problem is, it didn’t quite work. His extraordinary intelligence leaks through. This theory would explain why Molly seems so devoted to him, and gets so emotional when he ignores her. It breaks her heart.
Moriarty is the Master. Think about it. He keeps coming back, what’s to prevent him from coming back one more time? They’re both crazy psychopaths, and knowing that he would regenerate is why Moriarty doesn’t mind shooting himself. What if he regenerates into Sebastian Moran? (S3 villain)
What if Sherlock is a future regeneration of the Doctor, but his TARDIS got sucked into the Crack, causing him to forget it, and everything that went along with it. His adventures. All those times Sherlock just sits there thinking, he’s actually trying to remember something he should never, ever have forgotten.
In the parallel universe where Rose and TenToo are trapped, the Arthur Conan Doyle stories don’t exist, but the real Shlock does.
Also in the parallel universe, Rose and TenToo have two babies. One they name Sherlock, and the other Clara.