How exactly does one go about being a "Good" Assassin?
Only killing villians. I'm pretty sure most hero's are good even though they kill people.

As an assassin, shouldn't this class have Knowledge (Local) and/or Knowledge (Nobility)? And why Knowledge (Nature)?
Knoweldge (Local) is meant to be there seems I forgot it. Knowledge (Nature) is their so they can identify spiders and get Child of Araneae. I didn't want to add Knowledge (Nobility) as I thought it might cause it to have too many class skills

Weapon Proficiencies
If I remember right, one of the many issues with the Monk (in both 3.5 and Pathfinder) was that it's weapon list was so restricted. Why not just grant flat Simple Weapon Prof and then list the extras?
Your right I've changed it so it works with all Simple Weapons.

Assassin Techniques
Camouflage - You have a weird bit of grammar in the first sentence.

Child of Araneae - This feels a little weak to me as a 9th level feature. Maybe if the spider got half the Assassin's Sneak Attack dice.
Gave it better sneak attack, think I may have stuffed up the wording though.

Combat Trick - There's no spacing between this and the choice above it.

Drain the Fluids - And this works on any kind of creature? Elementals, Undead and Oozes?
I'll reword it.

Weapon Training - This is honestly a waste of a technique. Sure, normally the Assassin can't take it but the feat isn't that great to begin with. Maybe if the technique let you count as some level of virtual fighter or something.
Its the Weapons Training Talent from Pathfinders Rogue so it should be realitively balanced... I'll try and beef it up.

Widow's Toxin - This ability needs to be tagged. Also, poisons in Pathfinder don't have "initial" and "secondary" damage, that was a 3.5 thing. Viper for example.

Why does this key off charisma instead of constitution?
Sorry I'll fix.

Save Bonus against Poison
The name is honestly clunky, I'd consider renaming it. And it needs to be tagged as an ability. Also, does it apply to magical and supernatural poisons?
This has the exact same wording and formatting as the Assassin Ability of the same name. Thats why it is like how it is.. Why change what is canon in Pathfinder.

Advanced Techniques
You forgot to bold the name of this ability.

A Touch of Venom - The wording of this ability is a little clunky. You should word it more like, "If the Spider Blood Assassin successfully delivers an unarmed strike or a melee touch attack, they may use their Widow's Toxin Assassin Technique in addition to the normal effects of the attack."
I'll reword this.

Weapon Subtly
I think you misspelled subtly. This ability is something generally gained by a class earlier on than this point and once you add this with some of your other abilities, the class is starting to become MAD.
Changed it to Dexterity

This class has no capstone; what entices me to take all 20 levels of this class?
I tried to think of one but nothing came to mind.... I'll try again.

In fact, once I hit level 10 there's little to keep me in the class except for some numeric boosts and if there were some more Assassin Techniques, Advanced Techniques or feats that I really wanted for my build but hadn't gotten yet by level 10.
I'll try and think up some more Techniques and the Capstone.