What time zone do trains in Russia operate on? Does it make a difference between long-haul trains, electric commuter trains or international trains?
All trains in Russia for years have operated on Moscow time.
It's only slightly unsettling when you get to your train in Yekaterinburg and find out it's not there, but the upside is most of Russia is ahead of Moscow in terms of timezones, so worst case you'll arrive early, rather than late.
However, it now appears that is changing as of August 1, 2018 (source):
Tickets for journeys from 1st August, which can be purchased from 4th May, will be printed to display arrival and departure times in local times, however, tickets before this date will still show arrival and departure times in Moscow time.
Train stations will continue to have clocks that display both Moscow and local time for the current time.
RZD (Russian Railways) has announced that for travel dates from 1 August onwards it will abandon the long-standing practice of using Moscow Time for trains throughout Russia. It will finally switch to using local time, with the difference from Moscow Time in brackets, for example (MCK +5), in its timetables and on its website. Phew!
This is for intercity trains. Local commuter / suburban trains (eg in Novosibirsk, Yekaterinburg) operate on local time.