For certain journeys although, flights are a simpler option. For example, if you are on a short vacation and want to avoid the two day road journey to Leh Laddakh (although I highly recommend the road trip – you can read about it here) you can fly into the 3,700 m high altitude desert from New Delhi.
No trains in mountains
Owing to the difficult mountainous terrain in the upper Himalayas, namely parts of Himachal Pradesh, Jammu & Kashmir, and the seven sisters of North East (Manipur, Meghalaya, Assam etc), very few trains run these slopes.
For Darjeeling in West Bengal, for example, the railway line ends at New Jalpaiguri (NJP), which is a couple hours below Darjeeling. From there a shared taxi may be taken. (Read more about the Darjeeling journey here).
Read: Toy Trains in IndiaDepending on where you are, buses usually operate as far as there are roads in the mountains. Some hill stations which are inaccessible by trains have also small airports, like Bhuntar in Himachal Pradesh, and Leh Laddakh in J & K.
There is plenty of information on the internet about each destination. You may browse through my sectionDESTINATIONS for more details on where you are visiting.