When do I use a question mark with "Could you [please] ..."
Actually, sentences that begin with 'could', 'should', or 'would' are questions and should have a trailing question mark. Your original quote, "Could you please pass me the pepper shaker?", could be answered with a "yes" or "no." Although we usually use this syntax as a command it is not the same as the command "Pass me the pepper shaker," or "Please pass me the pepper shaker."
Etiquette tells us that it is more polite to ask for a response than it is to command a response.
According to "Basicwriting" course on Coursera: https://class.coursera.org/basicwriting-002/ there should be a period instead of question mark:
Use a period to end (1) declarative sentences, which state facts and opinions; (2) imperative sentences, which give commands and directions; (3) indirect questions; and (4) polite requests that are stated as questions.
... Requests that are stated as questions: Would you please point out Ulaanbaatar, Mongolia, on the map. Could you translate that sign over there for me, please.
According to my dictionary*, question is defined thus:
a sentence worded or expressed so as to elicit information
Also, one of my dictionary* definitions of could is:
a modal verb used in making polite requests
Thus, all "Could you…" sentences are really questions because
They are requests, indicating something is being asked for
A response or reply (verbal or not) is required of the person being asked
Examples:
- 'Could you please pass me the salt?'
'Sure! Here you go.'- 'Professor Calculus, please could you give me an extension on this assignment?'
'I'm sorry, Isaac, but you will have to turn it in at the same time as everyone else.'- 'Could you hold this for a sec?' Eric asked his brother.
(Response: Brother extends hand to hold item for Eric.)
'Thanks, bro.'- 'Here's the form.'
'Could you sign here, sir?'
'No problem!' (Man signs in indicated box.)
'All set. Thank you!'
Hence, you should always terminate any sentence beginning with "[Please] could you" with a question mark.
*New Oxford American Dictionary (2nd Edition)