There were three different boss characters that were originally planned to appear in this game: a scholarly elephant, a high society monitor lizard, and a technologically gifted mole. The former two were merged into Miss Decibel, while the mole was abandoned in favor of Penelope.
The trophy "Navigate Like Drake" is a reference to Nathan Drake from the Uncharted series.
The trophy "Ancient Warfare 3" is a direct reference to "Modern Warfare 3".
Collecting all 60 masks in game will unlock Cole's Amp from InFamous.
In the sewers of Paris, Bentley will say "Interesting... The last time I was in these sewers, I was a teenager!". This is a reference to the Teenage Mutant Ninja Turtles.
Hidden throughout the different time periods of Sly's ancestors, Clockwerk, the final boss of the Sly and the Thievius Raccoonus, can be seen perched peering around. Also, in "The Clan Of The Cave Raccoon," Clockwerk's eye can be found as a treasure.
During development, Slytunkhamen Cooper (along with Ancient Egypt) was planned to be in the game but was later scrapped due to the time frame of the game's release. Spoiler:But instead, Sanzaru made a secret ending with Sly in Egypt that goes straight to Sly Cooper 5.
Ghostbot, the team who animated the popular YouTube series Happy Tree Friends: Ka-POW!, also animated cinematics for Sly Cooper: Thieves in Time.
There are two treasures that reference Jak & Daxter and Ratchet & Clank. The Lutrela Nivadensis, found in "The Clan of the Cave Raccoon," is Daxter in a caveman outfit. Medieval Metal Man, found in "Of Mice and Mechs," is Clank with Knight armor on.