I had done the same quest prior, so I don't know exactly what happens, but supposedly you go on the hunt for it(by some other way obviously). If I had to rate them it would be something like:
Top half:
-Thieve's Guild, excellent quests in Markath and everything that has to do with
-Winterhold College, interesting premise and the Labyrinthian is cool.
-Main quest, eeks by on original trek up to Throat of the World and "The World Eater's Eyrie"
Bottom half:
-Dark Brotherhood - all but the last quest are boring
-Companions - no redeeming qualities here, short and boring and probably the buggiest quest line in Skyrim.
-Civil War - even worse. Take out a bunch of the same enemies in the courtyards of different forts, all coming from spawn points like COD or something. Nice to know that you win the whole "war" with 5 soldiers tagging along behind you.
If you want to count the deadric quests as one quest line then they go in the top half for sure. I didn't mind the general theme of guilds being on the brink of extinction in this game, but the bad outweighed the good. Mage's guild story and Thieve's Guild's quests stand out.