Most def, I joined the Stormcloaks last night and immediately after the first little "prove yourself" mission, a "JOIN THE LEGION: FAILED" message popped up. Join the Legion = Imperial Mission.
*******************SPOILER ALERT*****************
So one of the early Stormcloak missions is to storm Whiterun. It's pretty sweet, but I was worried my pimped out Breezehome and all my trading contacts in Whiterun would be lost by doing this, along with any future quests that the Jarl of Whiterun (Blarglarf or some ish) might give me. Well, we storm the city and make it inside the castle, where eventually the Jarl surrenders.
A new guy takes over and the ousted Jarl says something along the lines of "give me a few hours to grab my things, and I'll be out of here." I'm interested in following him to see if he goes to some random outpost on the World Map to call his home, so I can find him and his Wizard guy later in the game. I follow him up into the Jarl's quarters, and he eventually goes to this room, where he and other "key" members of Whiterun have apparently decided to call home:

I waited for about 24 hours to see if they'd leave, and they just moved to another corner of the room. Not sure if this is permanent, but for now, I'm calling this the Corner of Defeat. The Wizard still trades with you, so that's really all that matters.
Long Story Short, apparently when you overtake a city, the ousted government sets up shop in a corner.
*******************END SPOILER*******************
[This message has been edited by Baskin (edited 11/22/2011 10:59a).]