Comma questions keep cropping up online, and will forever, because the simple punctuation mark serves two different functions, which are blurred in usage. Some are necessary grammatically, some discretionary, and writers get muddled.
Let's deal first with the commas you are supposed to use.
Commas are required when two independent clauses are separated by a coordinating conjunction (and, but, or): John McIntyre has worked for thirty-one years at The Baltimore Sun, and he oversees the nighttime production of the printed editions. The comma is not required in an independent clause with a compound predicate: John McIntyre works at The Baltimore Sun and oversees production of the nighttime printed editions.
(Journalists, oddly, almost always omit the comma in the first case and unnecessarily insert it in the second.)
Commas are also generally required with introductory or concluding subordinate clauses: Since coming to The Sun in 1986, McIntyre has worked on the copy desk. Or: McIntyre works on the copy desk at The Sun, where he edits print sections of the paper.
Nonessential or nonrestrictive subordinate clauses in the middle of sentences, typically beginning with which, are set off with commas: McIntyre edits staff copy, which comes to the desk at irregular intervals, for the print editions. Essential or restrictive clauses within sentences, typically beginning with that, are not set off with commas: The copy that comes to the desk at irregular intervals is intended for the print editions.
Appositives, words or phrases that are not essential to the meaning of a sentence but provide additional information, are set off with commas. (You have just read one.) McIntyre, The Sun's night news editor, has been with the paper for thirty-one years.
The name of a state when running with the name of a city, or the year when running with a specific date, should be considered to be appositives set off with commas: McIntyre, a native of Elizaville, Kentucky, came to The Sun on September 2, 1986, to work on the copy desk.
The comma separates the items in a simple series: editing, proofing, and correcting. The final comma, known as the serial comma or the Oxford comma, is optional in some style guides. It must be used when necessary to avoid confusion—even The Associated Press Stylebook acknowledges that.
It combines with semicolons in a complex series: editing, the first step; proofing, the intermediate step; and correcting, the final step.
There are others—the vocative commas in direct address (Hi, John), for one—but these are the main ones to watch for.
But the comma, as David Crystal describes in Making a Point, his history of punctuation, started out serving a function like the rests in musical notation, indicating the length of pauses in a text being read aloud. To this day, the discretionary comma serves the same function, representing short pauses in the rhythms of spoken language. You will see it used, and will want to use it, in transcribing speech or mimicking conversational rhythms in prose (as in this sentence).