Clerks there is a scene where the two main characters have a conversation about the morality of blowing up the Death Star in Star Wars. They talk about how it was unethical to kill all the nonmilitary personnel on the Death Star, in particular the craftsmen who were working to complete it who were not doing anything inherently evil. A random person wandering by disagrees with their point of view - he suggests that those people knew what they were building and who they were building it for and that doing so had risks that they accepted. In essence he argued that by working for someone doing evil, even if you are doing very mundane tasks, you are doing evil and must accept the consequences.
This came up because Full Throttle was talking to me about setting up a business of questionable morality. His business idea is very much like the dollar auctions I talked about a few posts back and has equal merit in that it is simply a way of siphoning money off from suckers. He was wondering if I was interested in working for him part time in an administrative capacity - I wouldn't be doing anything directly to cause anyone harm but I would be supporting a business that is simply a parasite. It is a tricky question. This is an area where legality and morality diverge pretty severely because being a lawyer for a biker gang isn't likely to get you arrested but you are spending your life trying to make sure dangerous criminals evade justice. On the other hand being a secretary for a company that does underhanded things like bribe officials or fix bids doesn't seem particularly evil even if you suspect the wrongdoing taking place.
Strangely I think that the method of payment would make a big impact on my feelings about this proposal. If I was a stockholder working to make the company successful I wouldn't be at all interested in being involved in this sort of proposition. However, if I was just paid hourly and simply doing a job I wouldn't feel nearly so bad about it. How exactly I get my money for doing work perhaps shouldn't influence my moral impression of a job but somewhere in my mind it does; ownership implies greater involvement.
In general I think that anyone that has a really profound effect on an evil organization or who has a ownership stake in it is responsible for the things that organization does. If your job is irreplaceable or you actually get to decide the way things will be you must take ownership of that and recognize that the actions of the organization reflect on you personally. When you are entirely expendable and replaceable I think there is less onus on you to leave a company that does things that are wrong because your leaving will accomplish nothing; you will be replaced and never missed. I don't think that frees you completely from responsibility, mind, but I can accept that disruption of your own life to cause negligible harm to an evil organization may not be warranted. When you are just a cog in the machine you have a responsibility for the function of the machine, but only a small one.