"Did you file a Virginia return last year" - I didn't but my wife did. We filed separately, and are filing jointly this year. Is the question to me or to both of us?

This question applies for you, her, or both of you on a joint return.   

So in other words, I should say "yes" because one of us did last year?

Correct.  Virginia will use the information from prior year returns for verification.  (For example, in this case they will see you did file joint in the past).

This is our first year filing jointly.

The other problem is they did *not* use last year's information - there's line 3 in form 760c that it wants me to figure out myself.

I think the “using” your information reference above was more about the state’s e-file system comparing the information you entered related to filing a return last year to its files. 

It most likely uses this information for purposes of verifying your identity when you file electronically, as opposed to using any information to populate figures on a form.

@jpn124