Asking for the second/third recommendation letter, should I tell the referee he is writing the third letter?
This answer basically echoes the comment of Andreas Blass.

I agree that calling it the "third letter" may offend the professor, so I wouldn't use that phrasing.  But the general idea of acknowledging that the scope of the letter will be limited, and that you have other letters as well, seems fine.


  Dear Professor A,
  
  I am applying to grad schools, and I wondered if you would be willing to write me a letter of recommendation.  I know that the only course I took with you was BASK 301, and so I understand that your letter would only really be able to discuss my work in that course.  But if you feel you would be able to write a strong letter on that basis, I would greatly appreciate it.
  
  I am also requesting letters from Professors B and C, who will be able to write about my [other coursework / research / internship / relevant skills / etc], so I feel that between the three of you, a committee will be able to get a broad sense of my record.
  
  If you are willing, the letters would be needed starting on [date].
  
  Many thanks!
  
  Sincerely, etc.


If the course involved particular elements that you think would be helpful to discuss in the letter (e.g. a project on which you thought you did noteworthy work), then you can mention those specifically.