I went with the Stormcloak guy when we were running from the dragon. I was just wondering how this will affect me later on?
The choice between Stormcloaks and the Imperials is supposed to provide a little more immersion in the story: you choose a side, and while both sides have comparable quests, they take on a different flavor and will have different actors.
To this end, both the Imperials and the Stormcloaks have and 11-part quest chain concerning the Civil War that ravages Skyrim. The first few quests are almost identical, but then they branch off as each side wins (or loses) major fronts in the war.
And in general, choosing one side or the other makes things easier for you if the side you chose is in power.
For example, if your side controls a major city, you generally don't have to do any special favors for the Jarl in order to get permission to buy a house: it'll be given as a gift for siding the cause.
But the Elder Scrolls series is all about choice, and you're not going to be limited much by what side you choose. Choosing the side you most identify with will generally work out just fine.
But fear not, you didn't make a permanent choice when you went with Ralof (the rebel). You'll be able to play both sides until the last possible moment. You don't seal the deal until you swear an oath to either side by going to their stronghold city.
Additionally, there's one more chance to switch sides during the civil war:
If you're choosing the stormcloaks to ally with be sure to do the main quest "alduins wall" before fully committing to them, otherwise Delphine of the blades will become your enemy thus making the "alduins wall" quest impossible to complete. I learned this the hard way.
From what I've seen it doesn't affect it much/at all.
I've started 2 chars, one went with imperial and one with stormcloaks, the only changes I've seen so far is that when (whoever you're with) says we need to split up they both give you a quest, and it's to talk to a different person in Riverwood, if you go with imperial it's the blacksmith and he will give you some free items and limited info (and you find the imperial guy there, gives some more info but not much else) if you go with stormcloaks it's someone else in the village, gives you some free gifts as well but limited info. I'm guessing you can find the stormcloaks guy later in the game, but I don't think it affects anything beyond the first village.
The only thing I've found that is impacted is that if you pick Imperial:
Learned this the hard way.
protected by Community♦ Jan 14 '12 at 2:18
Thank you for your interest in this question. Because it has attracted low-quality answers, posting an answer now requires 10 reputation on this site.
Would you like to answer one of these unanswered questions instead?