What is the best way to travel between Munich, Salzburg, Swiss alps and Paris

There are a number of areas in Switzerland which could be described as the "Swiss Alps." Luzern, Lugano, St. Moritz, Appenzell, Lauterbrunnen, Zermatt, etc. Do you already have something in mind?

Thanks for the response. Not really, but by searching for most beautiful villages in Swiss Alps, I would like to somewhere like Wengen.

Another place of interest is Jungfrau region.

Ok, Wengen is in the Jungfrau region, also known as the Berner Oberland. Murren, Lauterbrunnen, and Grindlewald are also great places to stay in that region.

From Salzburg you can reach Wengen by rail in about 9 hours.

From Lauterbrunnen you can reach Paris by rail in about 6 hours.

For the Switzerland portion of your visit, you should look into buying a Swiss rail pass (family version) for yourself and your spouse. Your children will be able to ride free as long as they are with you; no extra pass or ticket needed for them.

nizreena, The Swiss Alps are the southern 50% of the country. As the others say, you have to decide where in the Swiss Alps you want to go. There are dozens of places to visit in the Alps, and you could spend a whole lifetime and never visit "all" of the Swiss Alps. If you have 4 places over 2 weeks, I guess you have 3-4 nights for each, so the usual suggestion for first timers is the Berner Oberland, which is the area between Interlaken (in the wide valley) and Jungfrau (a mountain).
The Swiss Alps absolutely must be visited by train, not car.
For an appreciation of the geography of the area see the "map" here: http://www.schlossoberhofen.ch/files/webcontent/Berner_Oberland.jpg
Red are rail lines, black is cable cars. The usual places to stay are Lauterbrunnen, Mürren, Wengen or Grindelwald. Mürren and Wengen are only reachable by train, no roads.

From the Alps to Paris, train is the obvious and fastest way. You can get a train from anywhere in Switzerland (including the Berner Oberland), connecting with a high speed train from Basel to Paris.

Another reason against a car is that if you hire a car in one country, you must return it in the same country or there is a very high surcharge.

Next question is train times and prices, and who to book with. Start with this webpage: http://seat61.com/Europe-train-travel.htm
and then proceed to the rest of that excellent website.

Thank you for all the valuable input. I have decided to stay in Wengen for 3 nights but still got to decide for 2 nights before that and 1 night after that. Want to include scenic train rides in to the itinerary. Where should I stay for the 2 nights before Wengen and 1 night after Wengen to accommodate the train rides and to go to Paris onwards?
thanks