In the "Disco" Arcade mode map, a record can be found on the mixing desk featuring the artist "Norgatious G". This is both a reference to the band Tenacious D as well as TimeSplitters' series composer Graeme Norgate.
The identity stolen by Cortez in the You Genius U-Genix mission is "Dr. Gordon". This is a reference to Half-Life protagonist Dr. Gordon Freeman.
In the "Scotland the Brave" mission there is an organ in the room before the castle tank boss that can be interacted with to play different tunes. One of these tunes is the theme from the Anaconda minigame in TimeSplitters 2.