During the लेखन of "His Last Vow", Moffat also wrote a scene about what Sherlock and Irene did after he rescued her from the terrorists in Karachi. However, the scene was never meant to be filmed.
Steven Moffat revealed recently that while he's not averse to the Sherlock/Doctor Who crossover, it's unlikely ever to happen. Never mind, though – there are plenty of weird and wonderful connections between the two shows already out there...