Stephen King, of all people, wrote about the 1978 version that he found some of the effects so disgusting he was surprised it was released in theaters without an R-rating.
Robert Duvall's cameo as the priest on the swing. Especially when you realize that he's actually the first pod person we see in the movie, mimicking the behavior of the nearby children without any concept of what is and isn't normal or appropriate adult (let alone clerical) behavior.
The scene were the schoolteacher, another early pod person, encourages the elementary school kids to pick the "pretty flowers" (infectious pods) on a field trip and to "remember to bring them home to their parents." The teacher's cold stare afterwards is particularly disturbing, as she glances around to make sure she isn't being watched by humans.
The realization that the ubiquitous garbage trucks driving around the city to collect strange, fibrous grey masses are picking up the digested husks of human bodies after their conversion to Pods.
Kevin McCarthy's cameo, in which he recreates the ending to the original film — only without the Framing Device that gave the original hope. He jumps onto Matthew's car, screaming that "they're coming" and begs them to listen to him. Naturally, Matthew and Elizabeth have no idea what the hell he's talking about. The man runs away, being chased by a large crowd, and then gets hit by a car.
Afterwards, Matthew calls the police to issue a witness report, but they claim they have no information about it. It's somewhat humorous how obstructive the police are and Matthew's frustration in getting nowhere, but it's clear that the pods are already in high positions within the city, hushing up anything that's inconvenient before they can make more overt moves.
Early on, Matthew goes to drop off his shirts at a dry cleaner in Chinatown. The owner privately tells him that his wife is different, saying "That not my wife!" in a clearly distressed tone. Later, Matthew goes back to the dry cleaner, and the owner says his wife is better now. "Much better now."
Dr. Kibner tells Matthew that he believes him and will help him get support to initiate a lockdown. Then Kibner gets into a car with Geoffrey and Ted, showing he's already been converted. Afterwards, Matthew tries to call a number of city officials, only to get runarounds. By this time, the invasion is firmly entrenched and there's little they can do to fight it.
Whenever a duplicate is "born". Special mention goes to the portion where Matthew, Jack, and Elizabeth drop off midway through the movie. A pod next to Matthew begins to crack open and give "birth" to his duplicate, which begins thrashing from side-to-side as it gets stronger. All the time, Matthew remains asleep, unaware of all this, as the panicking Nancy tries to wake him up before the pod completes the process.
When the pods try to break into Matthew's home, a number of them reach their arms over the door to his backyard while giving the inhuman pod scream.
After Jack and Nancy draw away the pod people, Matthew and Elizabeth try to blend in. The scene focuses on their legs as they make their way through a group of pods. Then the pods notice that they're unconverted. Their group gathers in number, with more people joining, until Matthew and Elizabeth break into a run.
This shot of Pod Dr. Kibner screaming from inside the lab cooler.
The duplicate that causes Elizabeth to break character while she and Matthew are trying to blend in — a mashup of Harry and his dog, who were sleeping near each other when the pod copied them.
Late in the film, Elizabeth disintegrates in Matthew's arms, and the duplicate version appears nearby.
There's a particularly chilling background event near the end - we see a group of (unconverted) children on a field trip being taken into a building. You can hear one complaining about how they don't want there to be another nap time so early.
The ending. Matthew returns to his pod-controlled office and blends in, whilst background events make it clear that he only slowed down their efforts to grow the pods and ship them out to the rest of the world. He takes a walk and is greeted by Nancy... then he points at her and pulls a Nightmare Face as he lets out a pod-man's distinctive howl. Nancy may very well be the only human being left in San Francisco, maybe even the world. Now she's probably going to suffer the same fate as her friends and her husband. As if that wasn't bad enough, the camera zooms into Pod Matthew's mouth, and the credits play without any music whatsoever.
of Pod Dr. Kibner screaming from inside the lab cooler.