My tickets used to get crossed out at the end of the workflow, but since I edited the workflow they no longer do that. I figure that I need to tell Jira somewhere which Status represents the "this ticket is completely done" state but I can not find anything like this anywhere in the UI.
This is one of the quirks that is really not clear, and it's really not intuitive for new users.
There are two fields we humans look at that matter here. (One of them isn't really a "field", but that's a talk for another day).
Jira strikes out "done" issues. Its definition is "the resolution is empty" = "more work needed" and "the resolution has any value" = "done". When something is "done" by that definition, it gets struck out.
So the short answer is "set the resolution on issues that are 'done'". How you do that is a bigger question, but to focus on your question, what you need to do is edit the workflow again and make sure a transition going into the status you have as "completely done" sets the resolution, either by asking the user for one in a resolution screen, or by setting it with a post-function.
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