How should I respond when my 3-year-old complains she is "by herself" in our family?
You daughter is absolutely right, of course. Then again, if she were one of the twins she would probably tell you that she's envious of her non-twin sibling, because she gets more attention as an individual.
These are the sorts of battles that you can never win if you argue the logic of the case. So what can you do?
First, let your daughter know that you take her concerns seriously. ("I can see that you're sometimes lonely at night.") Then work on ways you can address that issue. ("How about if Dad or I cuddle with you just before bedtime.")
At the same time, I'd give her ways that she can reframe her perspective on being the child who isn't a twin. ("No matter how old you get, you're always going to be their big sister. That's very special. Nothing can change that.")
You can expect this type of issue to crop up in some way from each of your children. Remember that it's a healthy way for them to vie for your attention. In general, respond by focusing on their emotions first instead of arguing the logic of their complaints.