They may not be in the majority of the books and comics, but whenever they do show up, they seem to be presented as a bunch of amoral nutters. And other than Isolation, I can't think of a single video game featuring them where they're presented as anything other than unrealistically over-the-top psychopaths who happily sacrifice hundreds of innocents to further their goals, or gladly feed random civilians to their pet Aliens in the name of "science".
I think their reputation as being cartoonishly evil villains in the EU is well-founded.