the Word Detective wades in (this is from one of his long issues that includes this towards the end, so I'll just shoot the whole thing in here):

Dear Word Detective: I am trying to find the origin of the phrase "call the shots" to use it in a sermon which asks the question "Who is calling the shots, you or God?" I have searched many web sites with no luck. -- Jim Mol, St. Mark Lutheran Church, Flint, Michigan.

Well, there's your problem. Haven't you heard? The web is over. Yeah, they all got fired and now they have to give back their Porsches and take jobs at Burger King, boo hoo. Anyway, there's been nobody home on the internet for quite a while. If you don't believe me, check out some of those news web sites. They've still got George Bush being President.

To "call the shots" means, of course, to be in control, to make the decisions, to run the show and to be the one truly in charge, especially as opposed to being merely a nominal leader or figurehead. Speaking of President Bush the Younger, and I report this solely to illustrate that definition, a recent poll indicates that around half of all Americans believe that someone other than Mr. Bush is actually "calling the shots" and running the government. Whether that perception is cynical or optimistic is, of course, best left as an exercise for the reader.

According to the Oxford English Dictionary, "calling the shots" seems to be a surprisingly recent phrase, having first appeared in print in the late 1960s, although it was probably in use as oral slang for years or even decades before someone thought to use it in print. An earlier phrase, "to call one's shots," meaning to announce exactly what one is going to do, apparently was current by the 1930s.

The real question, of course, is what all this shooting is about, and in the case of both "call the shots" and "call one's shots" the answer seems to be target shooting. In "calling one's shots," a target shooter (think Annie Oakley or the like) would announce in advance exactly where the target would be hit as a measure of his or her prowess. If someone else were "calling the shots," however, the shooter would be taking orders and hitting targets at that person's direction.

Note: Since the above column ran in newspapers I have been innundated with mail helpfully letting me know that "calling the shots" comes from the game of billiards or pool, wherein the player announces his shots in advance ("Eight ball in the side pocket" and so forth). Prior to researching the phrase, I, too, had assumed that it came from billiards, but the earliest citations I could find clearly refer to target shooting. That "calling the shots" occurs in billiards is clearly true. That it originated there is not.

http://www.word-detective.com/052301.html