He thanked me for what I (have done, had done, have been doing).

Question

That's all I had. According to me it should be HAVE DONE. But according to my friend it should be HAD DONE.

Answer 1

Because the first verb in the sentence is written in the past tense ("thanked"), I believe the correct answer is the past perfect, "had done". He thanked in the past, and what you did happened even before that (had done). "Have done" (present perfect) is more of a recent past.

Answer 2

Mark's answer is fine.

 

Any of the three forms you supplied in the question would be acceptable, under the right conditions.

Answer 3

"have" indicates past tense - something done in the past

"had" done indicates past perfect tense - something done before something else in the past.

 

I have done my homework.

I had done my homework before I went to the movie.