So, I just put up the Assassin Class for Microlite20, but, as the basic game doesn't include Alignments, I skipped out on a section regarding Assassins and Alignment.
By standard rules, Assassins should be of Evil alignment - and I'm not going to argue. You're not a Rogue, who can conceiveably use his skills at trapfinding and breaking & entering for Good. You're a person who kills people, normally for money. You're Evil. Deal with it.
Assassins also use poisons - another standard "Evil" mechanic. D&D Alignment has a funny relationship with poisons. In the original rules, it was fine for characters of any Alignment to use poisons (though there may have been a note regarding Paladins and their "Code of Conduct" - they're not very sportsman-like, after all...). In later games, using posion was an Evil act - regardless of intent.
Which, frankly, is bullshit.
Say you're a Paladin, fighting an Evil creature who is much stronger than yourself. Poison to weaken the creature levels the playing field, and I'd class that as a slight ding to your Alignment (Paladins are meant to suffer for their cause, after all), but not an Evil act.
Or say Mr Pally wants to take someone alive, with minimal harm - a very noble and Paladin-like act. Using a temporary paralysis agent is not an Evil act, no matter what the book says.
Now, if you use something that causes intense pain, suffering, and could kill someone? Evil. Poisoning innocents? Evil. (Yes, that last one includes poisoning the water supply of a horde of Evil creatures - not all Orcs are combatants!). If you can't justify it by your Alignment or Code, it's Evil.
Note, some Gods may not allow their Paladins or followers to use even non-Evil poisons - Kord, God of Battle and Hugeness, will think you're a pussy if you use that paralysing stuff. You're his Divine Agent - paralyse that fucker with your fists! Beat him into submission, in a fair fight - no cheating!
Now, 3.5's Book of Exalted Deeds did provide rules for "Ravages" - Good poisons which only work on Evil people.
However, they are stupid, and should be disregarded. They're still poisons, and the rules still apply. They're not Evil unless the intent is Evil.