Despite what EU tries to tell you, Star Wars is a story about good vs. evil, there's just no way around that. There are many examples of how Lucas crafted the movies to make it clear who are the good guys and the bad guys. The Jungian theory of the "collective unconscious," where one instinctively knows when something is good or evil based off of what humanity as a race has experienced over the millennia, is used to great effect.
Many elements of the Empire are taken from Nazi Germany. For example, Hitler had a cadre of specialized security and paramilitary forces that were called "stormtroopers." The look of Imperial officers was modelled after WWII uniforms of German officers. Additionally, the sound a Tie Fighter's engine makes sounds a heck of a lot like the shriek of a Stuka dive bomber. Try comparing this sound (
http://www.sound-effect.com/sounds/airplane/stuka.wav) (Stuka) with this sound (
http://www.filmsound.org/starwars/tie.wav) (Tie Fighter) and you'll know what I mean.
Darth Maul, with his demonic horns (a trait seen in evil beings in both eastern and western mythologies) and red tatooed skin, is unquestionably evil. The fact that the Empire and the Trade Federation both have robotic or robot-like troops without a recognizable face makes them much harder to associate with than their very human Rebel and Naboo counterparts. Count Dooku's staging of an arena fight that includes fearsome, bloodthirsty beasts is an obvious sci-fi version of the Roman Colloseum, where at one point thousands of humans and animals were slaughtered every day in gruesome ways to entertain a crowd whose lust for blood became increasingly harder to satisfy. As the deceitful Neimoidians snicker with a perverse glee and the crowd cheers when Padme's back is slashed, Dooku stands like Nero, callously looking on without even a hint of guilt or remorse to the carnage below.
Color plays a big role as well. The Sith all have an angry red color for their lightsaber, while the Jedi (in the movies anyway) all have more relaxing blue and green colors. The Empire has mainly shades of gray, black, and white, whereas the Rebels usually have a friendlier color scheme of green, blue and white.
At one point in the process of making Return of the Jedi, Lucas toyed with the idea of the Battle of Endor taking place over Coruscant instead of Endor. Rather than having the final duel with Luke and Vader take place on the second Death Star, the idea was for them to fight over a huge volcanic lake far under the surface of Coruscant, while the Emperor sat in a throne overlooking the sea of magma. With all that fire and brimstone, it's hard not to draw parallels to hell itself.
This is one of the reasons why I have such a hard time with the NJO series, I suppose. After all that the movies have tried to do to persuade those who see them that there are good and evil forces at work in the galaxy, some guy writes a book that tries to debunk the whole thing. As far as I'm concerned, it's pretty obvious that there is a dark side in Star Wars, and it's undeniably bad.