This is a practical oversimplification which will be right most of the time. For more detailed information see Mastery of the Tenses!
For an action previous to another past action.
- I had eaten before you came.
- Had you met before you started university?
- This morning I got dressed after I had showered.
To emphasise an earlier past.
- It was then she realised that they had met before.
- He was angry but I had warned him!
- By the time I arrived, she had left.
For reporting actions in reported speech.
- I said that we had eaten.
- You asked if she had seen the film before.
- They thought they had told you already!
For sequencing two related actions, but use is optional here - even if more 'natural'.
- Once he (had) finished the report he went home.
- After I (had) studied the chapter I tested myself.
- As soon as they (had) arrived, they unpacked their suitcases.
For separating two unrelated actions, emphasising that the first was completely finished.
- When I had tidied the house, I relaxed.
- Once I had prepared all the dinner, I got ready myself.
Used in IF clauses to describe hypothetical situations in the past.
In the IF clause of Third Conditionals.
- If I had seen you yesterday, I would have said hello.
- If they had won the match, they would have won the league.
In the IF clause of Mixed Conditionals
- If she hadn't told you, you wouldn't know anything about it.
- I would speak Russian, if I had been born in Russia.