Tom Nook - No. Greedy perhaps, but not evil. Here's a quote from Rich Amtower of Nintendo, with whom I agree:
"You think [Tom Nook]'s a jerk? That's too bad. He's actually quite nice. He's like that first boss you ever had when you worked your first job in high school or wherever... He's all about business, first and foremost, and if he doesn't always spare the time for pleasantries, that doesn't mean he's a bad person. He's just got a lot on his plate. Remember, he's hiring you, a fresh face in town without even a résumé. He's taking a big risk, and this alone should tell you a lot about his generous nature."
source http://www.1up.com/do/feature?pager.offset=0&cId=3172032
Catwoman - Debatable, but I'm going to say yes. While I would not call her an evil villain now, her character debuted as a villain in 1940 and was not really presented as more sympathetic/morally ambiguous until the 1990s or so. So she has spent more than half her time portrayed as a villain. She is on several "Top 100 comic book villains of all time" lists (Wizard magazine, Comicvine, IGN).
Light Yagami - No. Despite being a little conceited, he had good intentions originally, and his change over time could be considered due to the influence of the Death Note, making him in another of its victims
William Birkin - Absolutely yes.
*RE spoilers*
As one of Umbrella's top scientists, he willingly committed murder, torture, and human experimentation before becoming infected with his own creation. And it wasn't even Umbrella who infected him; after they stole his samples and shot him (preemptively betraying him because he was planning to betray them for his own gain!), he injected himself for revenge. After this point you can argue his actions as a G-creature were due to the G-virus, but it hardly matters as he was well on the evil side of things before then.
*end RE spoilers*
Gollum - No. A victim of the effects of the Ring. Although he kills his own brother prior to his transformation into the gollum-creature, there is no indication he was evil before then, and the urge to murder his brother did not come until he had contact with the Ring. His actions after that are all colored by the Ring's corrupting influence, but he still manages to help Frodo for a time.