Hawksmoor grabs Anna Steele, Lazarus' partner, in the Absurdly Spacious Sewer beneath the high school, then pulls her straight up & out of sight. This is like the ambush scene in Aliens where a soldier suffers a similar fate.
Hawksmoor is invisible to Lazarus during this, as the Marines could not see the Aliens in the scene in the movie.
Movie Deliverance - Banjo music and threatening Rednecks.
And a town flooded by a dam.
Giant tube worms on an abandoned ship at sea? Deep Rising.
Psycho - Lady DeMontford was dead all along. Her corpse can be seen rocking in a rocking chair in the basement of the Evil DeMontford Mansion.
The cyborg form that Digital Richmond becomes following Lazarus' death is a clear homage to the RoboCop films - his chaingun and rocket-launcher are both based on RoboCop 2's weaponry and the mechanical noises of his legs and arms are all sampled from the films.
During the prison level, Lazarus Jones makes his way through an underground maze featuring steam-pipes that fire hot steam jets and giant spinning cogs. After completing the maze he emerges in a shower-room surrounded from above by gun-wielding ghost guards. This is very similar to the underwater Navy SEAL incursion sequence from the 1996 action film The Rock.
Movie Wes Craven's Shocker - Agglin electrified prisoner.
A giant alligator in a swamp. A reference to too many movies to list. Just check the Internet Movie database for movies with 'alligator' or 'crocodile' in the name. Since it ends up being wrestled with, there's a vague allusion to the Crocodile Dundee movies.
Jerry Reed's Amos Moses. The one-armed swamp monster. "He could trap the biggest, meanest alligator, and only use one arm. Only got one cause the alligator bit it."
The ship's captain Kraken is turned into a giant multi-tentacled monstrosity that eats human souls. Cthulhu anyone?
There's a bell with a crack like the Liberty Bell: Lazarus rings it to free ghosts of townspeople.
Agglin, and the Warden's rant about no one escaping, are obvious references to the three Real Life prisoners who escaped Alcatraz Prison, Frank Morris, John Anglin and Clarence Anglin
The Pulse gun that Lazarus uses throughout the game strongly resembles the Calico M960A rifle, complete with a helical magazine design.
Colonel Fortesque's head plays the Real Life game Hot/Cold with his headless body.
The Cemetary area architecture, lighting and music are reminiscent of Ico.
Hawksmoor's castle has structure and color like the Queen's castle in Ico.
Tree roots growing through the DeMontford Mansion, like the tree under Decerto in the original Alone In The Dark 1992. The tree was the source of the mansion's evil.
shout-out to SCEE Cambridge's all-time best work, too! Surely Colonel Fortesque is a reference to - or, in fact, a descendant of - MediEvil's Sir Daniel Fortesque?
Sergeant (Sir Daniel) Fortesque's a sergeant In Name Only, similarly to how Colonel Fortesque's heroic exploits are really just historical embellishment.
Plus, when you defeat Captain Kraken, Colonel Fortesque admits that this is his first victory - Captain Fortesque never killed his opponent in MediEvil, instead falling during the first volley of arrows.
"The Fortesque family have been fighting man and boy for Old Blighty for over a thousand years. We've never let a little thing like death get in the way. Why, there's a Fortesque on every battlefield in the civilized world. Agincourt, dead. Waterloo, dead. Dunkirk, dead." - Colonel Fortesque, embellishing historically.
And they're both silly.
In the New School Theatre the poltergeists telekinetically raise chairs into the air and move them in geometric patterns. Psycho Mantis does the same thing in Metal Gear Solid. Here starting at 2:50.
There's a low-res poster of a bikini-model in the Janitor's office of the old highschool, much like the low-res "EXCITE! 1998" bikini model poster in the final level of the original Resident Evil.
When Digital Richmond's robot form unexpectedly falls through the floor, this is a Shout-Out to various other Survival Horror games that use this mechanic to advance the plot.