What effect does completing the quest line for the Stormcloaks have on other potential quest in the game? I basically ran through the entire quest line, but am worried that by doing this I have blocked some important quests from various Jarls ect that have been replaced. Is there any important quest I can't do now because I have Liberated Skyrim?

Don't know about what would happen if you completed the Stormcloak side since I haven't done it yet.

However, if you complete the Imperial side, the new Jarl of Dawnstar will not have a Stewart once they take the thone. So any quest that you do for the court in the Pale will not clear out of your journal... and clogged up journals annoy the ever living (expletive) out of me.

Other than that, I haven't ran into any quests that have their progression blocked after completing the Civil War storyline... yet.

Not really. When I did my first playthrough as a Stormcloak it didn't really change anything from what I've experienced as an Imperial or otherwise.
Only thing I could think of that you might not be able to do is Whispering Door, retrieving the Jarl of Markarths Father's shield, placing the horn Elisif gives you at the Talos statue, possibly the thing with Potema.
Most Jarl's things (seemingly) are minor.

I made the same mistake with my first character. Best is not to finish any guild quest before dealing with the small town quests.