Here’s a stage direction from the script for The Replacement:
It’s Xander lying unconscious where he fell. So who just went off with Buffy? Stay tuned. For this is only the…
BLACK OUT
END OF ACT ONE

The following was an alternative ending to Buffy vs Dracula:
Buffy arms herself with a lit torch, when Giles and Riley burst into the room:
The arrival of her entourage is the final straw for Dracula. He fixes Buffy with a final look, full of both pain and fury.
Dracula: “What …

The following lines were deleted from Buffy vs Dracula:
Dracula: “I know intimately what it is to be different. Human, but not quite…Of the world, but still an outsider…You see? We understand each other. Both of us are born of darkness, masters in the art of death-”
Buffy: “No. Hold it. …

The following lines were deleted from Seeing Red, after Buffy tells Xander it’s a little early for her to be drinking:
Xander: “The tyranny of the clock must be overthrown.”
Buffy: “So how many coup d’etats is that?”
Xander: “General Cirrhosis has seized control of the Liver Parliament.”

The following scene was cut from the episode Two To Go:
Clem: “We don’t have a plan. Don’t we at least need a plan?”
Dawn: “Buffy and her friends never have a plan. They just sort of… jump in and don’t know what they’re doing.”
Clem: “And this works?”
Dawn: “They …

This was a stage direction in the script for Lessons:
EXT. ISTANBUL-NIGHT
We see the (backdrop of the) city sprawling out beyond the rooftops.
and later in the script:
EXT. ENGLAND-DAY
No, really! Actual England. Not like that cheesy Istanbul.

The following was Dawn’s fantasy introduction to her class which was deleted from the episode Lessons:
Dawn: “…and my sister is a vampire Slayer, her best friend is a witch who went bonkers and tried to destroy the world, um, I actually used to be a little ball of energy until …

This line of Dawn’s was deleted from Same Time, Same Place:
Dawn: “Instead everyone just keeps secrets, and suffers alone, and then we’re supposed to be all sympathetic when they start ripping the skins off people or dragging their sisters to the basement! I may have some stuff to work through.” …

In the episode Two To Go, Xander, Dawn, Jonathan, and Andrew are running from the Magic Box, when Jonathan stops and says “I just need to breathe.” This could be a reference to Go Fish, during which Jonathon states that he is asthmatic.

In Older and Far Away, Xander says the line “…And now we can’t leave. Only thing missing is a cornfield. There … there isn’t a cornfield, is there? This could be a reference to the 1989 movie Field of Dreams about a group of baseball players who purposely lost the …

In The Wish’s alternate reality Giles states that, “In order to defeat Anyanka, one must destroy her power centre. This should reverse all the wishes she’s granted, rendering her mortal and powerless again.” However, that turns out not to be the case. While, indeed, Cordelia’s wish is …

In Beneath You, Buffy asks Principal Wood why exactly she got her job at the new Sunnydale High. She asks him if he maybe he enjoyed her work at the DoubleMeat Palace and Principal Wood replies with, “I’m a vegetarian.” Well, as we all know, Buffy learned in season …

The script for Conversations with Dead People mentioned The First Evil by name, even though it was not yet mentioned in the actual dialogue of the show.

A stage direction in the script for Bring on the Night was:
NOTE: It is VERY important that Giles does not touch or be touched by anything. He can walk and talk - but he can’t fiddle or cuddle or caress. Got it?

The following line was cut from the episode Showtime:
The First (as Eve): “And Chloe, honey… you don’t have to worry about getting called to be the Slayer before you’re ready. You’ll be dead before that happens. All o’you.”