Travel between Munich and Salzburg

Buy a Bayern-Ticket from a ticket machine at the airport and take the train all the way. The ticket costs €29 and will cover 2-5 people traveling together on the S-Bahn and regional trains all the way to Salzburg. Take the S-Bahn from the airport to Muenchen Ost and a regional train from there to Salzburg. If your plane arrives on time, you should be able to get to Muenchen Ost in time to catch the Regional-Express train that departs at 15:50 and arrives in Salzburg at 17:42. See the detailed timetables on the German Rail site. The ticket will NOT be good on either EuroCity trains or Railjet trains from Munich to Salzburg.

Best? By cost or schedule? Actually probably best either way. Two to five people can travel by train from Munich airport to Salzburg for €29 with a Bayern-Ticket, total (€14,50 ea for 2p). The trip by regional train takes about 2½ hrs, including 20 min ± transfer time in Munich Hbf, and there is one regional train/hr. If you want to pay more, hourly express trains make the trip from Munich Hbf (you still need to take the S-Bahn to the Hbf) in about 1½ hr. I saw shuttle buses from Munich airport to Salzburg. They take about the same elapsed time but only run every two hours and cost much more. They might take you to a specific hotel. The one I saw had to be booked in advance, an iffy thing when you are arriving by air. I would use this webpage for Bahn schedules. It has a few more options. The link in the post above takes you there eventually; why not start there? Here is the Schnellbahnnetz (S-/U-Bahn) map of Munich. "Ost" is German for East and is the concentration point for S-Bahn trains coming in from the east before going through the S-bahn tunnel under the town. Like the Hbf, on the western end, it also serves regular trains - express and regional. There are two tracks in the airport S-Bahn station, separated by a platform. The track (Gleis) on the RH side of the platform (coming from T2) is for the S1, which enters Munich from the west, stopping first at the Hbf, then going through the tunnel to Ost. S8 leaves from the LH side and goes around the east side of Munich, enters the tunnel at Ost and then goes to the Hbf.

There are six S-Bahn per hour from the airport. For four of them, the ones at :11, :24, :31, and :44 past, it really doesn't matter which one you take or whether you go to the Hbf or Ost; you'll be able to catch the Regional Express (RE) to Salzburg. The ride on the S8 to Ost is a little shorter, and the tracks are closer together, but the RE only stops there for a minute or two. The RE seems to consistently use track 8, but check the schedule board. On the other hand, the RE originates at the Hbf, so you can board it earlier and find seats, but it is a longer trek from the tief Bahnhof to the main track area. The RE leaves from the Holzkirchenbahnhof (Gl. 5-10), about as far from the S-Bahn station as you can get. Holzkirchen Bhf is attached to the south side of the main shed area. Go out along track 11 until you get to it, near the end of the covered area. Don't take the :51 train. It goes first to the Hbf, arriving too late to catch the RE. Then it goes to Ost, arriving there too late also. However, if you take the next S-Bahn, the S8 leaving the airport at 4 min past the next hour, it gets to Ost in time to catch the RE, but is not in time to the Hbf.