Difference between "had come" vs. "came" vs. "used to come"

1 = Had Come Talks about an Action ( in this sentence "come") which has happened before another thing in the past.

Example for Had come : Imagine a situation in which 2 things have happened and we're talking about them :

1 = I did my homework ( at 9 PM)

2 = I watched TV ( at 10 PM)

5 Hours later i want to report these things to my Mother :

Me :Mom, I watched TV at 10 !

Mother : what about your homework ?

Me : I had done my homework before i watched TV.

2= came Talks about an Action which happened in the past and IS NOW FINISHED. and we're not talking about any other action.

3 = used to come is a different Grammar which talks about an activity that you regularly did in the past and no longer do (it) now.

Example : I used to smoke ( Means : In the past , smoking was a habit of mine and it no longer is)

The Main Source of the answer is Cambridge Advanced Grammar in Use(Third edition)

Good luck.

The first one with the past perfect describes an action that took place earlier than another action in the past. Therefore, we would normally use it to refer to a single incident. If we wanted to refer to something that was recurrent prior to a reference time in the past, we'd use the past perfect continuous.

Is he the doctor who had been treating your bad knee before you moved to Atlanta from New York?

The simple past can be used to refer to individual incidents or recurrent/habitual events. Absent context, we cannot know which it is.

Are they the ones who came over for lunch that day when I was visiting?

Are they the ones who came over for lunch every week after your committee meeting?