When the gargoyles throw Sherlock (Johnny Depp), Watson (Chiwetel Ejiofor), and Juliet (Emily Blunt) in a crate on the ship, it has the company name "Moffat & Gatiss". This is reference to the creators of Sherlock (2010), Steven Moffat and Mark Gatiss.
The moving van at the beginning, behind the car carrying the gnomes, is labelled "Sherrinford Movers". Sherrinford was the original first name for Sherlock Holmes, before Sir Arthur Conan Doyle changed his mind. The name went on to be the institute on the BBC series, Sherlock (2010), that housed the Holmes' sister Euros.
Sherlock Gnomes was modelled after Basil Rathbone, who played Sherlock Holmes in fourteen movies between 1939 and 1946.
The Doll Museum is named Doyle's after Sir Arthur Conan Doyle, who created Sherlock Holmes. The entrance to the museum also says that the address is 221b. Holmes' address is 221b Baker Street.
When Sherlock Gnomes (Johnny Depp) and Moriarty (Jamie Demetriou) fall off of Tower Bridge, blue fireworks go off behind them, resembling a pouring waterfall. This is a possible nod to the iconic image from Sir Arthur Conan Doyle's story "The Final Problem", where Holmes and Professor Moriarty fight to the death on the ledge of the Reichenbach Falls, Switzerland.