I know how to reference a variable from a quest script. But what about from another script that is not part of a quest?

For a quest it's..

MyQuest.myVariable or

set MyQuest.myVariable to 1

But what about if the script isn't attached to a quest?

Same thing, but it has to be on a persistent reference. myPerRef.myVariable.

edit: At least, I think that's how it's done. I think it's more common to have that item copy it's variables to a quest script that any other script can access.

Showler's correct.