I believe the proper etiquette would be to request a pause by saying "pp," leaving it to the opponent to pause when he/she has finished the action they are currently working on. This removes the irritation of the pause without warning, and also allows the opponent to mentally prepare for the break in gameplay.

Following immediately after the request or pause (depending on how quickly the opponent can pause the game), an adequate explanation should be given. Adequate is up to the discretion of the opponent.

No more than 5 minutes should ever be taken in time out.

Upon returning from your emergency or situation, be sure that your opponent is not afk. If he is afk, then you must now provide the same courtesy he gave to you by waiting for his return. If he is not afk, tell him that you are back and ready to go when he is. Let him resume the game.

In summary:
1) Request a pause by saying "pp." The decision of pausing is left up to your opponent.
2) Give a proper explanation for why the pause is necessary.
3) Get back as quickly as you can. Do not take more than 5 minutes at most.
4) Tell your opponent that you have returned. If there is no response, then wait until your opponent has returned as well.
5) Tell him that you are ready when he is, and allow him to resume the game.