During the Iron Tech raid, when the Punisher uses a special kill on one of the yakuza members, the line "Oh my God! They killed Kenji!" can be heard. This is a parody of a popular line from the TV series South Park.
The car that almost run over the Punisher after completing the Crackhouse level has the license plate "ASM 129", which is a reference to the Marvel comic book, The Amazing Spider-Man #129 (Feb. 1974), the issue that the Punisher made his debut.
The game data file named "tables.vpp" contains much of the scenario data; one of the things included in it is part of the credits and other scenario data from Red Faction II!
On May 31, 2005, the English version of The Punisher was put on the infamous German index by the BPjM. For more information about what this means and to see a list of games sharing the same fate, take a look here: BPjS/BPjM indexed games.
Early in the game in the Lucky's Bar level, you hear some mobsters talk about Daredevil, asking who would win in a fight between The Punisher and Daredevil. One of the mobsters replies that such a thing is not possible, because Daredevil is a comic book character.
Much later on in the game, when you play in the Fisk Industries level, you can hear an enemy something along the lines of "Daredevil never did this to us!" when The Punisher shows up; much later on, you see Matt Murdock (Daredevil's secret identity) try to defend The Punisher when he's being interrogated by the police in a cutscene. Seems like the writers didn't make up their minds on deciding if the game exists in the normal Marvel universe or outside of it.
Along with the interrogation scenes being censored in black and white and zoomed in when you killed a criminal, the PC version had blood removed from the interrogations as well (most notably in the face smashing and punching interrogations).
Also, THQ cut some rather disturbing quick kills. One involved The Punisher using his knife and plowing it into the side of a criminal's head from behind (you had to have had a shotgun or rifle selected as your current weapon to get it). Another involved The Punisher coming up from behind and giving the criminal a bullet enema (ie. shooting the criminal up the butthole with his gun).
Fanmade patches were created to restore some of these interrogations, along with the gore missing from interrogations.
There was some controversy in the US when the ESRB threatened to award the game an AO rating. Later, THQ decided to tone down the game by making the "Special Interrogation" scenes black-and-white. Because of this, the game was rated M.
Initially US version was given an RC rating. The MA15+ rating for the OFLC in Australia was given after the game was "revised".