During the 5th level, on Displace International Headquarters, when in an air vent you can hear two guys talking about the new Prince of Persia game, made by Ubisoft.
Sam and Douglas Shetland's first face-to-face meeting in this game takes place in a bar. In Splinter Cell: Pandora Tomorrow (2004) Shetland offers to sit down and have a drink with Sam some time.
The first Splinter Cell game to be rated M.
In the Fourth Level ("Penthouse Level") there are two TVs that show still images from Splinter Cell: Pandora Tomorrow (2004), the second Splinter Cell game.
In the news report prior to the Hokkaido mission, one of the scrolling headlines reads: "Front man of punk band Kesshin sent to jail". Kesshin is the band that composed the music heard on radios in various parts of the game.