verb tenses

It all depends on context. Technically, none of them are truly correct because each one needs a comma between "happened" and "and" in order to separate the two independent clauses.

Aside from that, all three sentences make grammatical sense. You just have to decide which one to use depending on the situation. I'll see if I can get this to make sense...

The first two are almost completely interchangeable. You could use either if, for example, you fell off your bike and then went to see a doctor. Then you tell him what (had) happened, and he examined you. I think the second sentence addresses the issue of tense more correctly, but no one will think twice about your meaning if you use the first. The omission of "had" is really more of a result of native speakers' laziness, and everyone understands it.

The third sentence is trickier. Try this scenario:

You fall off your bike, but you only get a small scrape on your arm. Your mom forces you to go see a doctor, even though you know that you don't need to. When you get to the hospital, you tell the doctor what had happened and that he really doesn't need to examine you. (Call this point A.) The doctor agrees with you, but your mom insists that he or she examines you anyway. Then, the doctor examines you and finds that you are fine.

Ok. If you were explaining this situation to someone else and you wanted to refer to point A, then you could say, "I had told him what had happened (at that point in time), and he examined me (anyway)."

I really hope that makes sense...

Bah, a number of typos in that post:

In the third paragraph, "tell" should be "told."

In the fifth paragraph, the first "examines" should be "examine."

Although Sean has made some sense, but I think making scenario to describe grammatical point is almost misleading. I prefer the comprehensive definitions.
I think, too, all three are right, depending on what the speaker means.
However, a Past Perfect tense [had had] refers to a verb that took place in the past and was finished [itself and/or its influence] BEFORE another past tens (in whatever form) either in the same sentence or in the whole context. Draw a line; mark a pint on it and call it Present; mark another point and call it Past Perfect. Mark a third point between these to marks. Whatever action (in a verbal sense) beginning from the second mark and ending before the 3rd mark could be conjugated as Pas Perfect IF you are ALSO mentioning the time between the 1st and the 3rd mark in the same sentence or the same context.
The exception is the indirect quotation that will change the tense one step back towards the past. i.e. “he has done it.” Would be quoted as “She said, he had done it.”

Native speakers who know grammar, help!

I just found this: http://www.englishpage.com/verbpage/pastperfect.html

gossun, your explanation is gibberish to someone who isn't deep into grammar rules and syntaxes, and for something that looks like a simple question of which sentences are correct, you complicate things way too much.
Giving actual examples is the best way to answer a layman, and if he is a grammar expert he will understand anyway.

Shouldn't the question be "Which of the following is grammatically correct"?

they all work. the first one sounds like for example you got hurt in a game and someone came out to examine you on the field. the second one is like after the fact... say you got hurt in a game and this was taking place at the hospital... "had happened" means that it was in the past. the third one means the whole event took place in the past like you were hurt in a game and went to the doctor, he examined you, and now you came home and are telling someone about it. they all work, they are just different tenses.