After taking over holds and towns with the legion or the stormcloak, can you still access the place, or your house in that area? Does it change anything with your house or the area? Can you still visit/do quests in it?
The only major difference after a town is captured is that the Jarl will change (Solitude is an exception to this).
There is no need to worry about your house, potential quests, or followers - the only casualties of war (aside from Tullius / Ulfric) are nameless "Imperial / Stormcloak Soldier"s. The Dohvakiin is unaffected.
It's worth noting that some NPC houses (such as Heimskr's) may be inaccessible after battles have been fought in their towns. Therefore, certain random quests that require access to them may be bugged.
It doesn't make your house unaccessible, but you'd better finish up any outstanding miscellanous quests you have for the Jarl of Windhelm before finishing the civil war (and the Jarl of Riften, if I recall correctly), otherwise you won't be able to finish their quests.
Defending Whiterun from Stormcloacks will destroy several houses (The Talos preacher's and Severio Pelagia's) and kill a named NPC (Severio Pelagia, who buys vegetables from you). You will also be unable to do special quests for deposed jarls, and their replacements will not offer unique quests, but they will make you a thane.
Also, a named, (minor) quest-giving Thalmor justicar will be relocated from Markarth Keep to the adjacent Hall of the Dead, if the Stormcloaks take the Reach.
I would suggest that you make sure you finish everything else in the game before you proceed with the civil war. I have experienced very nasty bugs like Legate Rikke not talking to me, General Tullius not talking to me, Soldiers not massing for attack outside Windhelm, Palace of Kings fight sequence not activating, etc., - I am guessing this is because I did not finish up on meeting Aventus Aretino, retrieving the White Phial, etc., before embarking on the Reunification.