In general, it's a distinction between stative (being) verbs versus non-stative (action) verbs. Be, have, want, need, know, love etc. are stative verbs and you would use those with "wish" in the simple past form. Example: I wish I knew the answer. I wish I had a million dollars. I wish I were taller. Verbs that show action are usually used with "wish" in the past perfect form. Example: I wish I had run the marathon. I wish I had gone to the movie. I wish I had kissed him when I had the chance. But English is full of exceptions and non-standard uses, so you will hear "I wish I ran the marathon yesterday" (non-standard but doesn't sound too strange, especially here in the south). You also need to take time into account like on Peachey's answer when you are talking about "to be" to mean actively be existing someplace. "I wish I were at the concert" means that the concert is happening right now. "I wish I had been at the concert" talks about a concert that happened in the past that you did not attend.

For a start, when you use "wish + past perfect", you are talking about the past. The others are about the present.