The World Government is led by the Gorosei. They ordered the destruction of Ohara, but seemed genuinely upset about having to do so. While undoubtedly a bad thing to do, they appear to have been working towards a greater good. Whatever happened during the void century, they're walking a fine line between Dark Justice and Moral Justice to keep it a secret.
The World Government controls three powers. The Marines, Shichibukai and Cipher Pol.
So far Shichibukai have proven to be pretty villainous. The exception so far being Mihawk.
The Marines appear to be a mixed bag of corruption and honor. At the top of the food chain we have Sengoku. Don't know much about him personally but we do know that in his front yard he has Enis Lobby, which sports a laughable excuse of a courthouse and has no problems with manipulating giants with lies. He's also the guy who gave the obviously incompetent Spandine a Golden Den Den Mushi.
Below him are the three Admarials. Ao Kiji seems to be a genuinely good person. On the other hand he gave the even more obviously incompetent Spandam a Golden Den Den Mushi.
The other of the three Admarials we've seen is Akainu, who order the destruction of the civilian ship escaping Ohara… just incase. Somehow murdering a ship full of people who's homes you've already unjustly destroyed seemes a bit excessive.
Of the Vice-Admirals there's Monkey D. Garp, who's obviously a cool guy and clearly doesn't belong in the rank of Vice-Admiral. Jaguar D. Saulo was a Vice-Admiral too.
On the flip side, it takes six Vice-Admirals to perform a Buster Call, so there are at least a dozen of them that are comfortable with blindly bombarding a target into nothingness without knowing the reason. We saw that one of the Vice-Admirals during Enis Lobby killed dozens of Marines to keep the Straw Hats from escaping and personally executed one of his own crewmen.
Down to Captains we've got guys like Smoker, who have to deal with craploads of red-tape to do their jobs, and guys like Morgan, who make statues of themselves and kill little girls.
Out of Cipher Pol, Spandam is clearly evil. He's a self serving, woman beating, ego-maniac with no regard for any human life other than his own. Under his orders, CP5 attacked a Judicial Ship using Franky's ships. That's all sorts of criminal there. Judging between his behavior between then and his time commanding CP9, odds are good that illegal/immoral activities that serve nobody but himself were common place.
As for the other members of CP9, Lucci and Jyabura were clearly evil. Both self-acknowledged sadists. The only member of CP9 who seemed to be a genuinely good person, in spite of his profession, was Kaku.