House of Horrors was my overall favorite quest in Skyrim. In general, the Daedric quests represented the best Skyrim had to offer. Few side quests or faction quests even came close to matching them.
I tihnk Oblivion had the best quests. Skyrim is an intense diappointment, especially if you're a rogue and like to do Thieves Guild, and you get... that. I don't mind trying to make the thieves more, well, scummy, but compared to stealing an Elder Scroll it was silly and boring. Although, there isnt really anything TO steal in Skyrim *sigh*.
I'm leaning towards Oblivion as having overall better quests, but this might get my vote as single best. I didn't realize this quest even existed until my 3rd character. And IIRC to get all the details you had to actually work at it, I think you could have bailed partway through and still technically completed the quest.
This quest plus the slow unfolding of the Dagoth Ur/Tribunal story and your part in it (if you were the reincarnation of Nerevar) blew my mind in a way that no TES game has before or since. I also didn't know you could actually meet and talk to Vivec. So discovering that after a hundred hours of play, and after reading about him in books, was amazing.
Yep, you could say "screw this quest" at any point, ignore trebonius, and do other quests, then usurp Trebonius's position instead. The only goal you're given is to find out what happened to the dwemer. It involves a lot of gathering dwemer written works, and finding scholars that can help point you in the right direction, but it's very satisfying to complete it and freak out Trebonius.