If booking far enough in advance, it's cheap to travel by train, and not a long journey. I bought my ticket recently online between
Munich centre and Zell am see from the German rail site: www.bahn.de (Translated versions are in English and other languages.)
I missed the cheapest price on the outgoing journey from Munich, which had been 19 Euros, but the next price was still good at 29 Euros. 29 Euros and 19 Euros returning. The booking fee was less than 4 Euros. Total: Less than 20 pounds each way, averaged.
Times are pretty good for resort transfers, especially going across a border - learound 2 hours 45 minutes usually. I didn't see the option to change in
Salzburg as I've read some people suggest, the bahn.de did work out one change, in Woergl.
Though it does take 50 minutes roughly to get from the Munich airport train station to Munich Central Station (trains every 10 minutes or so).
Do book these tickets online or by telephone (numbers from bahn.de) well in advance as the prices go up substantially near the time, to nearly four times the inital price (19 Euros to around 75 Euros single or a few more). So it's not such a good option if you are arriving at Munich without a prepaid train ticket.
Train tickets sold online are e-tickets, which are printed yourself, and you must have the card you paid for the ticket with when you are on the train journey.
Seat reservation seems to be a few Euros extra on this route, though it is not necessary. Though that may be for the German part only, there was something mentioned about seat reservation in Austria being more complex, so I didn't bother.
There is a regular bus to
Zell am See if you are flying into / coming from Salzburg which is not expensive. (Sorry, I don't know anything about
Innsbruck transfers - but try rail - both www.obb.at and www.bahn.de).
There are some more comments about getting to the Zell-
Kaprun ski area on a Tripadvisor forum page:
http://www.tripadvisor.co.uk/ShowTopic-g608666-i10668-k866923-How_to_get_from_Munich_to_Zell_am_See-Zell_am_See_Austrian_Alps.html
If going to Zell / Kaprun: There is a ski pass (SuperSkiCard) which is hardly more expensive at all than the Z.-K. area pass. It gives access to a range of good sized and small resorts including xxx and
Saalbach Hinterglemm. EDIT: I had read elsewhere that
Mayrhofen was included, but I don't think it is. It's too far anyway to travel unless you are shifting your base (but then again, leaving at 6 a.m., and up for a 3 hour journey there and back in the evenings, it's a great day trip if you're driving.)
BUT the really good Kitzbuehel area is included in this area ski pass. There is a train from Zell am See to Kitbeuhel which takes less than 50 minutes. (Last year I went to the joint second largest European ski areas,
Serre Chevalier, Southern French Alps [joint 2nd with around 9 other resorts albeit] & these transfer times were quite regular from one mountain to another, 55 mins. from furthest of the 4 mountains by bus, often 30 mins. from one mountain to the next but one along.)
There is a bus from Zell am See to Saalbach which leaves Zell around 8.20, mornings, (also later buses) and only takes 32 minutes to Saalbach.
Saalbach Hinterglemm more or less doubles the ski area available on quite quick public transport from Zell. Also smaller nearby resorts are covered in this SuperSkiCard pass's area - like
Leogang.
Also, it's quite strange, both this SuperSkiCard resorts pass and the Zell-Kaprun area multi day tickets don't give a lot of discount over 1 and 2 day tickets. So you wouldn't lose much to buy tickets in groups of 1 or 2 days, for Zell-Kaprun only, or Saalbach Hinterglemm, or, as there's not much price difference anyway , the SuperSkiCard resorts pass. And if taking a day or two rest, you wouldn't be missing out on a good discount which many ski resorts give for 6 day or longer tickets.