They mean the same thing. However, if the person you are speaking with was not there himself, you would not say "I wish I had been there too, because neither one of you were there. If he was just telling you what he read or heard it was like, you could say "Oh, I wish I had been there, don't you?"

I wish I had been there *too* is emphasizing that there were other people there, but you were not there. Saying just "I wish I had been there" is fine.

I wish I had been there too will be used if : someone had described a situation they were at, and they mention - "I wish you had been there with me." This is a good time to say, "I wish I had been there too." If they describe a situation they were at - and they do not say anything about you, then it is fine to leave off the too or keep it. If you here of a situation from long ago - even before you were alive - hundreds of years ago or whatever: leaving off too is preferred- of course. In these situations it is still fine to imagine yourself there "I wish I had been there when____."

Almost identical. If you were talking with your friends you might say, "too" if you'd wanted to join in with them, say to a Black Sabbath concert :)