Long War
It's called the Long War because it truly is loooooooooooooonnnnnnnnnngggggg. That is not taking the mickey either. It has been going on for 10,000 years and see no signs of abating.
It is the ongoing conflict within Warhammer 40k between the forces of the Chaos Traitor Legions who turned to Chaos during the Horus Heresy and the mess of a super empire that is the Imperium. Considering they seem to have been calling it the 'Long War' all along, could this be the Chaos Legions admitting the 'weak' Imperium is not so weak after all? If you ask them this though you are likely to be tossed into one of Nurgle's favourite pox pits.
It is a rather confusing term since noone is quite clear who is and isn't part of the conflict, what battles are covered under it and various other details about it. For example: Do the space marines that have turned to chaos since the heresy count as being part of the Long War? Do the lost and the damn and the daemons of chaos count as taking part as well? Does every conflict fought between Chaos and the Imperium automatically count as part of the Long War? It tends to be one of those terms that people toss around casually without referencing it further. This could be GW's stubborn refusal to let too much fluff out of it's forbidden depths.
Actually there is likely a very good reason the Long War gone on as long as it has, due to the leadership of a certain armless failure.....