For me, I liked the Raven Rock quest from the Morrowind Bloodmoon expansion, where you helped a settlement to grow from bare roots, and turn into a thriving town, that you could own a house in. I also liked the Cropsford quest line from Oblivion, where you helped a small group of settlers who were trying to build their homes on land that, unbeknownst to them until it was too late, was amidst a goblin tribe war. I hope there will be a quest line like that where you can see a settlement grow up, because you helped them. Or vice versa, where you hurt the settlement in some way that made it so it didn't grow like it could have.
What about you?
(Edited because I called the settlement by the wrong name. D'oh!)