'¿' doesn't exist in English.

"Where is my black pencil?" is the correct way to ask the question.

"...where my black pencil is" is not a full sentence, but a subordinate clause which can be treated as a single noun. Note that the latter form is not a question. Ex. "I don't know where my black pencil is."

Neither "When her car come?" or "When come her car?" is correct. Depending on what tense you mean, the question should be "Where will her car come?", "When does her car come?", "When is her car coming?", "When did her car come?". The subordinate clause versions are "...when her car will come", "...when her car comes", "...when her car is coming", "...when her car came" respectively.

"Why is your hair black?" is the correct question. "...why your is hair black?" is the subordinate clause version.