As Laura mentioned (and Lee usually does), I would recommend a Bayern Ticket.
I assume you plan to return to Salzburg? This would be a great deal, especially since I gather that more than one of you will be making the trip. You can also make a trip to Andechs, since it's at the end of its line on the S-Bahn. Not that I've done this... ;-)
This way, you don't have to make a specific train, in case you're having - or NOT having - a great time at Oktoberfest. You DO all have to travel together, though.
Your price would be 23€, plus 5€ per each additional person. Five people total are allowed on a single ticket. So, two people could travel R/T b/n Salzburg and Munich (and on the Munich S-Bahn, subway, trams and buses) for 14€ each. Three people would be 11€ each, and four would pay 9,50€. Not too shabby. Train times are basically the same, so no difference there. Just buy the ticket at the Salzburg train station (from a machine, or for probably about 2€ extra from an agent).
Even during Oktoberfest, these trains won't sell out, so don't let that color your decision. You'd think they'd be crazy full, but in my experience over several trips it has never been the case. You might consider skipping the U-Bahn and walking to the grounds from the train station, though. It's usually less busy and less crowded. If you get to the platform and it's a mob scene, just walk.