If taking the narrow-gauge train ride from Kalka to Shimla, sit on the right. However, when Shimla is around forty minutes away, from then on, left is better: you can get a view of Shimla, with its yellow cathedral conspicuous from afar. If your train is delayed so that you can get this view of Shimla after the sun has set and it's relatively dark, then all the better: the view is magnificent.
If the train is packed, overall, choose right over left (while going from Kalka to Shimla). For down journey, do vice versa.