The correct answers are Could you tell me where the bakery is?, Do you know what time they open?, and I was wondering if they sell chocolate croissants.

In indirect questions, we use standard sentence word order (Subject + Verb) instead of question word order. We do not use auxiliary verbs like do/does/did, and we do not invert the subject and the verb.

Therefore, "where the bakery is" is correct, while "where is the bakery" is incorrect in this context.