Alchemy and light armor and you are set.
The biggest, most important of all is sneak. At high levels you are near-invisible. It's the most important tree of your build, no doubt, and you'll pretty much want everything in it, although I find that 2/5 for the first perk is enough for me, and I'm at skill rank 94 at level 38.
Light armor and daggers are indeed key. Also, your best light armor is dragonscale, so smithing is also recommended in my book. You can also improve the armor with it for even more protection, and you will pick up glass smithing on the way to make some neat weapons. In the endgame, you will reach the cap on armor (80%). heavy armor gets there faster, but is heavier.
I personally disagree on alchemy being a must. My backstabber doesn't use it. The potions I randomly find are sufficient. It's very viable though, and a good way to go if you like.
Next is up to personal taste. I use the following:
Archery: you need some sort of ranged attack, trust me, and archery has a x3 sneak attack perk you need to pick up on the x15 dagger sneak attack route, so it's perfect. Also, you can fire an arrow at a location to distract enemies. They will investigate where the arrow landed. Lasltly you can trigger traps with it. In my opinion it's a must.
Smithing: Making, and then improving, your own weapons and armor is perfect and powerful in the game. It's very easy to level by making iron daggers and leather bracers. You can take it straight to 100 if you are so inclined, although that may unbalance the game somewhat. In your favor, that is. Still, not that fun. I personally set a rule I will never buy crafting materials from merchants, and only will use what I find in the wild. It also gives an incentive to hunt deer and explore mines. It also ensures you keep in line with how powerful the game expects you to be.
Restoration: A quick heal in a tight spot is divine. Also has 100% spell blocking shield spells, which help you if spellcasters have spotted you. As an added bonus there are perks that speed magica regeneration and save you from death. All in all it's a good package.
Others I don't use:
Illusion: It has muffling spells which make sneaking easier and at higher levels invisibility. Very powerful when your sneak is low. It also has perks that make spellcasting silent. Ideal for daggermagi. I used the muffle spell quite a bit at lower levels so I could sneak up to enemies which would normally notice me, but never invested perks in it.
Lockpicking: You will be doing it a lot. And I mean a huge lot, no matter what class you play. It doesn't add all that much though, but it removes a frustration. *damn you master level locks...* Still, by the time you encounter master level locks you will have enough money to buy a thousand lockpicks anyhow. there are a few interesting perks that promise more loot, so it may be rewarding. There is, however, one birthsign standing stone that allows you to bypass most locks. Still, there's better signs out there, which makes lockpicking the only way to open locked chests.
Pickpocket: Sometimes nice to get a key in my opinion. I find that a silent dagger to the back is a quicker road to Rome though if you want something from a person. Still, it can be fun I suppose. The 100 carrying capacity perk certainly appeals to everyone. But I'm not impressed.
Enchanting: It's good, I'll be honest. I prefer smithing though. Combining the two will make one too powerful in my personal opinion.
Speech: So now you got the loot, but you need to sell it. Speech is mostly about bartering, and will help you get more money for your goods, allow you to fence goods to more people, etc. For the thief in you there's the 'bribe guard' perk.

Things to avoid:
Magic: Unless you want to be a daggermage, I'd stay away from destruction, alteration and conjuration.
Block: You want a quick and silent kill, not a prolonged battle. Go dual wield.