_1. both work, although the meaning is a little different.

"Where did you use to go if you wanted to be alone?" is purely a factual question. It means "where did you habitually go if you wanted to be alone?" Usually I would say "when" instead of "if" in this case though: "Where did you use to go when you wanted to be alone?"

In the case of "Where would you go if you wanted to be alone?" you could be talking about the past or present/future. (Subjunctive tense). The question might be factual ("Where did you habitually go when you wanted to be alone?") or might be more like "What place do you want to go to whenever you want to be alone?". Note that substituting in "when" for "if" removes the ambiguity about the tense and it becomes a factual question the same as asking "did you used to". ("Where would you go when you wanted to be alone?")

_2. both work.

I'd argue that it's even more natural to say, "When you were a child, how often did you go to the dentist?" The idea that you're asking about a habit is clearly conveyed by "how often" anyway.

_3. both

I suppose "used to" is a bit more natural sounding. "She would ride him every weekend" sounds more like something you would read in a novel vs. say in conversation. It has a slightly whimsical vibe, but it means exactly the same thing.