Who actually wins?

nobody knows yet.

There is no established canon of who won yet. You probably have to wait until TES 6, but they will probably disregard it and have no one win.

There are theories and hope, but that is about it. Here is my theory: http://www.gamesas.com/topic/1469980-afterthoughts-on-the-stormcloak-rebellion/

Is ESO set after Skyrim? Is that game even canon at all?

I'm gonna say they went ahead with the ceasefire, and Skyrim becomes independent.

Just my guess.

ESO is set about 1000 years before Skyrim, in the 2nd Era, before the Septim Empire rises.

Both.

Well, whoever you sided with, that is. The way I see it, when you have something in an Elder Scrolls game with different outcomes, there isn't a "canon outcome" and a "non-canon outcome". Either could be canon. That's why they normally avoid giving specifics about events with different outcomes in past games, I believe.

Alduin's defeat will likely take precedence over it.

it will cause a dragonbreak

It'll be interesting, that's for sure.

Most likely there'll be some unbalancing event that takes place outside of the game to make your actions irrelevant. Ex: The Imperials acquire some game-changer in the battle for supremacy against the Dominion. They'll acknowledge that somebody won but a side got a canonical advantage afterwards that outweighed the Last Dragonborn's help or opposition.

Personally I'd prefer to see an independent Skyrim because it would be interesting to see how the Nords and the Empire are forced to work together against the Aldmeri Dominion anyway. I'm all for seeing a return to independence for the provinces and possibly broken down even further than that.

There was a civil war, and some business with dragons...then the Aldmeri detonated some sort of magic and the whole province collapsed into black reach. The few survivors tell different stories so no one really knows who won, and since Skyrim played no part in the second war between elves and men no one really cares who won.

Don't think it matters.

Can't see the CW even getting a mention in TES VI.

It's only an optional questline in TES V.

Still a cornerstone of the game's setting

I can see a rumor or two flying around in the next TES.

Mostly everything that you are able to do does not get mentioned in the next game.

Next game will probably be set in a province that's to preoccupied with it's own troubles to care what happens in Skyrim. The civil war is to small for a Dragonbreak, Daggerfall had around 6 different factions you could give the totem too, each greatly affecting Tamriel.

I don't think they can just ignore it unless they have a very long time break, so no record of who ruled in Solitude between the dragon crisis and the second elf war remains. Otherwise they have to bury it, which I would prefer...whole province collapses like Winterhold did only better, no one survives who knows or cares about the results of the civil war.

The Dragonborn fails and Alduin eats everything so everyone loses...the elves are the first to be pooped out and history eventually repeats itself.

THey could also make the next game happen at around the same time (the first 4 games happen within about 50 years of each other) in another place (here is hoping for Summerset) where the Civil War does not really mean much and so would not be a huge factor of the story.

The amount of topics made about the civil war makes the main quest seem like a side questline and the civil war to be the main thing.

Maybe if fighting Alduin actually felt important...but yes, that was the same for me too. Which given the sameness of the civil war...lets just say Skyrim survives off of exploration big time.

The CW isn't really optional as doing the MQ without joining a side still requires you to negotiate a temporary truce. I feel that the CW events could have a major impact on the next game, likely the end of the Empire or something similar.

I see it being told as both sides being worn down by war to the point that the Thalmor easily comes in and mops up what's left, thus making both Skyrim and Cyrodil too weak to do anything about it, leaving Hammerfell the last free nation and the setting for TES 6

I would say neither and both. we likely will not know, so I tend to stay of the fighting.