[Franky Family]

1) Anju & Kafei Marriage - Majora's Mask

2) Protecting Romani Ranch - Majora's Mask

3) Chuck Quizmo - Paper Mario

4) Pit of 100 Trials - TTYD

5) Big Goron Sword - Ocarina of Time

 

[Ascend]

Mass Effect 2. The biggest side quest ever, consisting of even more side quests, which also have sidequests.

 

[Dreamlord]

The Bloody Baron, TW3.

 

[Kadayi]

The Bloody Baron, TW3.

^ I'd probably go with that. For the most part TW3 quests were leaps and bounds above anything in most other titles from that period, but TBB was heads and shoulders the best of the sidequests in the game for sure.

 

[Zog]

Oblivion - The killers in the mansion part of the Dark Brotherhood quests.

 

[GreyHorace]

A Sackful of Fluff (The Witcher 2) - Geralt accepts an unusual request of collecting a hundred harpy feathers for a 'collector.' The results are... interesting to say the least.

When the Cat and Wolf Play (The Witcher 3) - In a game with a plethora of amazing and interesting sidequests, this one stood out to me the most. If you ever wanted to know how shit a Witcher's lot is in the world, this quest boils it down for you.

Equine Phantoms (The Witcher 3: Blood and Wine) - The quest that shows you how deep Geralt's bond is to his trusty steed Roach, to often hilarious results.

I Remember Me (Mass Effect) - A quest exclusive to a Colonist background Shepard. Here, Shepard helps a young survivor from the colony he/she grew up in. A touching and emotional side story that sheds light on Shepard's past.

The Long Road (Dragon Age 2) - Could qualify as one of the most hilarious quests ever written in a Bioware game. Hawke helps Knight Captain Aveline with a unusual request regarding one of her subordinates.