We've been to Moscow a few times in the past few years. We've travelled with Czech airlines via Prague, small airport in Prague and short layover, also it's 2, 2hr flights
The latest trip we went with KLM via Amsterdam, very short layover (45 mins) but the airport is big and we had to run for it. KLM staff at the airport were great though and very helpful and our luggage arrived with us which was good.
We've also gone via London with BMI which is my least favourite, the Flight from London is about 4 hours which makes it seem like a longer journey
Be prepared to queue for ages when you arrive at Passport control. They are very thorough,