It isn't matter. Is it matter? <<< These two are wrong. You'll mostly hear phrases like: "It doesn't matter" - used to show that something isn't important. "What's the matter?" - used to ask what's wrong with someone if their visibly annoyed/upset. "Does it matter" - used to ask if something is important or not, or to avoid telling someone something. E.g. Mum: "Where were you?" Son: "Does it matter?"

Actually the other two sentences are also correct but they have a different meaning. In those sentences "matter" is a noun meaning any physical substance. For example, at CERN they spend a lot of time studying dark matter.