The way I intend to play through the main quest, civil war and dark brotherhood quests is as follows:-

- Main Quest

- Dark Brotherhood

- Civil War (for the stormcloaks)

The main reason why I think this order makes sense is it allows you to play the really cool Season Unending quest and remain neutral until the dragon menace is dealt with. Playing the Dark Brotherhood questline before the civil war as a Stormcloak supporter also makes sense because it seems absolutely crazy for Vittoria Vici to be having her wedding in a Stormcloak controlled Solitude or indeed for the Emperor to be visiting there so casually which I doubt Ulfric would entertain.

I'm wondering though is the Emperor ever mentioned in the main questline or Civil war questline AFTER he has been killed in the DB questline or does some dialogue change to reflect the fact that he's dead?

Dosen't the game get boring if you plan everything ahead of time and do things in a strict order? Personally i think Skyrim shines when you just let events occour naturally, but whatever floats your boat.

But to awnser your questsion i don't recall the emperor ever beeing mentioned during the main or civil war quest, i also think it would make sense if you do the CW and DB questlines at the same time.

The Emperor is only mentioned during the Dark Brotherhood questline. As far as I know he isn't mentioned anywhere else in Skyrim both before and after his assassination.

He is mentioned in the Imperial Army Oath. But when he dies, he is left out of the Oath