At first, yes, the interrogation scene was a little chilling. But a lot of things were fiction that it kinda throws me off. They have Allen wearing wing walker which never happened. Lots of things in that scene was made up to implicate Allen to the viewers which killed it.
But 1 scene that is in the directors cut was getting the search warrant. That scene at least had some accuracy in what they discussed with the DA. It had Toschi, Armstrong and Marty Lee with the DA on speaker phone. I loved they at least sald Allen doesn't resemble the SF composite and Toschi says he never had confidence it was accurate. Still wish they showed the composite as its iconic.
I also felt chills in one scene after the cab murder where Graysmith is watching TV and the newscaster says "the Zodiac Killer has come to San Francisco."

The basement scene isn't just the scariest in the movie, it's one of the most effectively scary scenes in any movie, ever!
I also felt some real chills during the SFPD's interrogation of Arthur Leigh Allen in the factory. The ambient noise throughout is very effective, as is John Carroll Lynch's demeanor. The way is voice suddenly drops an octave as he looks at that detectives to say "I'm not the Zodiac." Made me shudder!

Yeah but I felt like the song kinda killed it for me. Only scary killing was the lake case if had no music.
In reality the cab murder scares me the most. It's in a small neighborhood and the thought that a serial killer is outside your home is scary. That's why I had to walk the area when I visited SF.
I have been to a "lovers lane" with a few girls in my life since knowing about Zodiac but never thought about it. To this day I'm afraid to even be an ber driver because of the cab killing.
And while I love the way the cab scene was shot, that music after the shooting again takes away a bit.

Well, when I watched Zodiac I didn't know anything about the Zodiac killer. So almost every killing scene was pretty 'scary' because I had no idea what would happen.
The first killing scene of Darlene Ferrin and Mike Mageau had the most impact on me. I felt so bad for both of them that a 'random' person fired on them, with the result of the death of Darlene Ferrin.
After that I couldn't take my eyes of the screen the entire movie because I needed to know who did this.

Schleiben28 - I found the Berryessa scene downright disturbing. I looked away from it in the theatre and fast forward through it on DVD.
I'd put the first scene ahead of the abduction, but that was also pretty creepy.

Oops, I meant Johns. Not Johnson.

I think it's a toss up between the Lake Berryessa murders and Kathleen Johnsons abduction on March 22, 1970.