Should I use was or were: It _ the eyes

In agreement with the previous answers, the missing word here should be 'was'. Another way to think about it is by reading back over the sentence, and noticing what verbs are used in the earlier part of the sentence:

it wasn't the face that scared me, it _ the eyes

Wasn't is short for 'was not', so expanding the contraction, you can see 'it was not' used earlier in the sentence. Reversing this negative gives you 'it was', which goes in the second half of the sentence

It’s always “was” with “it”

That’s because the pronoun “it” only ever replaces a singular noun; and “was” goes with singular things. If we need a pronoun to replace multiple things you use “they” in the subject case and “them” in the object case. Noting that these can also be used of multiple people but it’s extremely rude to use it to refer to a singular person.

“It” here is replacing the thing that did the scaring. Not the face, the eyes.

But, wasn’t the thing doing the scaring the eyes, and don’t faces usually have two of them? Well, English can be tricky when referring to collections or sets of things - you can refer to the set as a singular whole “the eyes”, or its just as valid to refer to the individual members “those eyes”. So there are two legitimate ways of constructing your sentence:

1. It wasn't the face that scared me, it was the eyes.
2. It wasn't the face that scared me, that was those eyes.

If there was more than one face, you could also go with: it wasn't those faces that scared me, it was those eyes.

The choice is up to the speaker/writer, but the first sentence has a better feel because it is keeping the same number of things throughout: one person me, one face, one (pair of) eyes and it is more impactful due to the repetition of “it”.