Both Jill and Chris receive new alternate costumes in Deadly Silence. Jill's is a white wife-beater, a police hat, and a pair of very short cut-offs, which very much resembles Poison's outfit.
The virus-infected crows that peck unfortunate victims (such as Forest) to death may be a shout out to The Birds.
The Chimeras, human-fly hybrids, are a clear reference to Cronenberg's The Fly (1986). Supplemental material even confirms they are born from human women injected with human/fly embryos, which parallels Veronica's fears of her baby would be like.
In fact, pretty much every enemy in the game is a reference to some film. The Neptune is clearly inspired by Jaws. The Hunters are basically Velociraptors with their "clicky" walk, ability to open doors, and ungodly shrieks. Giant spiders were a staple of the 50's giant monster movie genre. And, of course, the zombies come from George A. Romero's Living Dead Series.
The flamethrower that Chris uses is modeled after the one that was used by the Marines and Ripley in Aliens, in addition to that, he sports a similar haircut to Hicks, and has a similar role in the story as a member of a corporate funded paramilitary organisation who has to keep himself and his squad alive against numerous monsters that are being bred by the very corporation that funded their respective organisations, as well as having to deal with a double agent within his own group.
Another likely reference to Aliens is that the S.T.A.R.S much like the Colonial Marines, were ambushed by monsters while searching for missing civilians, in both scenarios, the first team member to die has the last name Frost, the Remake took the Aliens vibe even further by giving the S.T.A.R.S members body cameras.
The moment Rebecca is screaming while cornered by a Hunter is very reminiscent of the scene where Lambert dies in Alien, Rebecca can also die if the player as Chris fails to save her.
Numerous nods to the game's Spiritual Predecessor, Sweet Home, including but not limited to:
The introduction of the game's first zombie, which is a reference to the "Man" enemy's intro
The door loading screen, which is almost completely lifted from the older game
The use of a slide projector for exposition of the mansion's dark history
Jill's lockpick, which is identical in use to Emi's special key