For a stealth based character, the Dark Brotherhood has the best rewards in my opinion. Here is why:
*SPOILERS*
1.)Muiri's Ring- It makes potions and poisons 15% stronger. While this is not really significant, one can simply disenchant this so that they can make powerful enchanted clothing that stacks well with Alchemy.
2.)Nightweaver's Band- Sneak is 10% better and Destruction costs 10% less to cast. This supports two essential skills for a Nightblade archetype. Not to mention, you can increase your enchanting skill because of the double enchantment.
3.)Olava's Token- When you receive this, you will have to meet Olava in Whiterun. She tells your fortune. This is where you look for an assassin, only to find his corpse lying with a much more powerful version of the Shrouded Armor. You are immune to Poison! This is a plus if you don't have the Dragon Priest Hevnoraak's mask(100% Resistant to both Poison and Disease). Also, bows do 35% more damage! This stacks very well with an Archer type character.
4.)Shadowmere- This is the most powerful horse in the entire game! He can be very much of a lifesaver in numerous situations.
5.)Blade of Woe- Out of all the daggers in the entire game, this has the most base damage! Also, it is enchanted with an Absorb Health by 10 points enchantment. If you have a very high Pickpocket skill and have the perk where you can take equipped weapons, you can get this early on. Plus, near the end of the storyline, there will be another Blade of Woe lying on the ground. This means you have a duplicate of the best dagger in the game! This stacks beautifully with Assassin's Blade, as well as Dual Flurry and Dual Savagery.
6.)Followers- At the end of the Dark Brotherhood storyline, you have access to two or three followers, depending on a choice you have to make later on in the game. The first two that you are automatically awarded are Dark Brotherhood Initiates. They can make things easier for you. Then there is Cicero. A number of people on here are constantly annoyed by his Character. However, he is perhaps THE BEST FOLLOWER in the entire game! His sneak skill is 100. He is the only follower who WON'T screw things up by making both you and him discovered in any dungeon or any place that is filled with enemies. Also, he's a level 50 NPC.
The only other storyline that has just as good of a reward, if not better, is the Thieves Guild. Simply, it's because of the Nightingale armor. It supports the sneak skill, as well as illusion, fortifies stamina, and adds a resistance to frost. The enchantment is level-based. If you want the best results from it, do not get the Nightingale armor until you are level 32 or higher.