In Skyrim I'm playing an agent of the argonian court, so I was thinking. Do we know anything about the situation in Argonia and Morrowind, the relations between the dunmer and argonians or anything about the black marsh governement? Secondly, which side would Argonia support, the empire or stormcloaks if any at all? And in the main quest we have to choose between the greybeards and the blades, who would the agent support?

The argonians have invaded Morrowind near 200 years ago, what the current state of the occuption or the war (if any) is, is completely unknown. It seems like the Argonians still occupy part of Southern Morrowind, most likely former Dres territory. The Black Marsh government is still the same as it has always been. I don't know which side they would support. They themselves moved out of the Empire, so the Argonian government likely isn't to big a fan of them, outright hatred or hostitilies don't seem to be present either. From an ideological perspective it might be logical that they would think the Stormcloacks have the right to support themselves, from the perspective of their own citizens however the Empire would likely be more beneficial as possibly racists Nords aren't a good thing for the Argonians. Now the first wouldn't require sending an agent into Skyrim, the second however just might.... This is of course speculation as we simply don't know.

They likely wouldn't choose a side between the greybeards and the blades either, they have no reason to do anything like that.

Black Marsh did invade Morrowind shortly after the Red Year, and drove the dunmer out of Morrowind and kicked out the Thalmor from Black Marsh. As for how far they went, they did go at least as far north as the former city of Vivec, but for actual lands they took, it was only contested southern Morrowind territory. Since then, they've been extremely isolationist, and the current leading group is the An-Xileel, as of Infernal City.

For the sides they'd take and so on, I don't see them caring much at all for the plight of others, save for their Marsh-brothers and sisters. So, no one in the civil war, and as for the Blades/Paarth, I'd leave that to your discretion.

Concerning the last one, this I ask more game-wise. Let's say the argonian agent turned out to be the dragonborn (hero of tes V), and at one point he has to choose between the blades and the greybeards. Who should he choose?

It depends entirely on the personal idea's of that particulair Argonian... Does he or she believe Justice knows no expiration date, does he believe one can redeem itself, does he believe that a possible future danger needs to be eliminated, does he believe in taking risks? You have to decide for yourself. There is no reason to assume any one entire race would have a different opinion then another. From a government perspective however I can imagine all governments would want Paarth dead, simply because he could be a threat to their government sometime in the future and shows absolutely no sign of wishing to ally himself to one particulair province.

Something tells me things are not going well for the leaders of Black Marsh at the time of Skyrim, a shadowscale in the DB sanctuary says that he was an assassin in service of the High King of Argonia (as all shadowscales are) but the shadowscale order has fallen apart, and so he is at the DB sanctuary. Only weak/insane governments would disband an assassin order of invisible lizards.

Indeed.

Anyways, Black Marsh has always been a Dendrocracy.

Trees tend not to be very good at bureaucracy though. Too much paper and all that. They do have to delegate.

If the Argonian Court wanted to maintain its independence of the Empire, it would be interested in seeing the Stormcloaks win, as that would weaken the Empire, and the Stormcloaks presumably have no interest in threatening Black Marsh. So, it would make a lot of sense for an Argonian agent to aid the Stormcloaks. Also, that goes along with my sense that the Dunmer in Skyrim would tend to be pro-Imperial -- you'd expect some hostility between Black Marsh and the remnants of Morrowind, and for them to be inclined to line up on different sides.

Well, first of all, you probably wouldn't be in Skyrim. You have no reason to be; the Argonians are isolationist, and the conquest of Morrowind was more out of revenge than anything. The Argonian State would have no reason for you to be there. In fact, I highly doubt the Argonian State even has agents of any kind. I guess the Shadowscales could have filled that role, but that order disbanded long, long ago.

I love you guys.

You may as well argue that there's no reason for there to be any Argonians in Skyrim at all, because it's a long way from Black Marsh, and the climate is so radically different that you'd expect them to find it almost unendurable. Really, given how much intrigue goes on in Tamriel, the idea that one nation would dispatch an agent to another to advance its interests is hardly a stretch.

Come to think of it, when real-world nations have pursued isolationist policies, those times and places seem to be popular choices as sponsors or as targets of secret agents in fiction.

See, the Argonians aren't your average nation. They want nothing to do with anybody, if possible.

But if the Argonian Court considers the Thalmor to be the greater threat, weakening the Empire would bring the Thalmor ever closer into direct conflict with Black Marsh, and loss of a potential ally against the Thalmor ?
Its not like the Nords are the kind of people who would work with outsiders and the buffer zone is nice.

The thing with a biggest bad, they bring the biggest of rivals together. When it comes down to it, the nations of men will band together if it means defeating a common foe, who has already shown its metal. With Black Marsh, the Trees need to ponder, and learn from the Saxhleel in distant lands. After all, the Saxhleel are bound to the Hist, and the Hist's roots go deep and far.

If worse came to worse, the Hist would try to intervene. As for now, they may see either outcome as being beneficiary in the end.