As kind of a counterweight to the 'Best Action Scenes' thread. Which scenes do you find particularly moving?
Personally I think the description of the Zetetic Elench's search for their lost ship in Excession is a extremely plaintive piece of writing. That sense that they knew the search was almost certainly going to be fruitless, but that they carried it out anyway because there was always a chance that they might find the ship or evidence of its destruction, and so to not at least attempt to do so would be unthinkably callous. Makes me think of modern-day SAR crews who'll spend days looking for people lost at sea.
In Look to Windward, the descriptions of Lasting Damage's experiences of the Idiran War, and pretty much any scene from the POV of Major Quilan.