One of Jill's extra costumes mimics Regina's appearance from Dino Crisis, which was developed concurrently.
The ending sequence involves a missile strike on the city in a sequence that greatly resembles the end of the first Return of the Living Dead.
When you reach the power station, you may get a Live Choice as to how to deal with an incoming zombie swarm. One option is to turn on the power to the exterior fence, which results in a sequence a lot like the ending of Return of the Living Dead II.
Speaking of Return of the Living Dead, we see zombies rising out of graves in this one, something the first film did to great effect (and while raining, to boot).
The Nemesis itself has some similarities to The Terminator, as both are nigh-indestructible monsters who pursue their victims through a urban environment. Speaking of...the Crowning Moment Of Awesome page mentions Terminator cocking a shotgun one handed, this is exactly what Jill does.