I'm just going to run through a mental list of all the games/franchises I own and decide if they really are evil or not.
Crash Bandicoot - Yep, Cortex is evil. But he's just a lackey for Uka Uka anyway, who is also evil.
Spyro the Dragon (original series) - Yep, every boss evil, save for possibly Gnasty Gnorc, who is simply trying to deal with the extreme racism shown to him and his entire species by the dragons. Yes, in the first Spyro game, you play a racist who wants to enact a 'Final Solution' against an entire species of creatures that are forced to live in a (ghetto) Wasteland.
Warhammer 40K Fire Warrior - Well, we're dealing with Chaos as the bad guys here, so yes, evil. The Imperial Guard and Space Marines aren't included here because they have a (admittedly fragile) truce with the Tau, and this only breaks (and is subsequently fixed) because of the Chaos presence.
Final Fantasy XII - Arguably, no, the villain isn't evil. Yes, he is an imperialistic douche, but the entire plan (and Venat's plan too) revolved around freeing humanity, viera, moogles, bangaa, etc. from the rule of a worse race of god-like creatures that were using these races throughout history for their own purposes. The expansion of the Arcadian Empire was just a side effect, albeit one that was pretty bad, though even then the Arcadian citizens seemed perfectly happy witht heir rule, and Vayne did at least make an effort to get his new subjects to like him, and tried to earn their respect...
Assassin's Creed - Depends on your worldview. I do side with the Assassins here, but the Templars do genuinely believe they're doing what's best for humanity as well, even if they are trying to get power themselves. I can't really see the Templars as evil, simply greedy and misguided, but also genuinely interested in the wellbeing of humanity, even if that wellbeing would be given through lies and deceit.
Alan Wake - It's the Dark Presence. And Mr Scratch. Yep, 100% pure evil. No questions.
Bioshock - Well, again, this depends on your worldview. Nobody, I'd say, is evil as such. Everyone simply has their own conflicting views, and instead of talking about them like reasonable people, they decide to start a civil war. This applies to Bioshock 2 as well, and the effect of said war on every character involved. Those who aren't involved are simply mentally disturbed, not evil, and the Splicers are all simply the survivng addicts of a pretty bad drug culture. No evil here, just political extremism and lack of self control.
Final Fantasy XIII - We can look at it two ways here. On the one hand, all the Fal'Cie want is to find a way of bringing back their own goddess, which any religious person would see as admirable. On the other hand, the plan does involve the deaths of millions of humans, the near extinction of the species, and the manipulation of humanity over hundreds if not thousands of years. I wouldn't really consider the Fal'Cie to be evil, as such, but they certainly push the boundaries.
Fallout 3 - The main villains here are the Enclave. I don't see them as being evil, again, it's simply political extremism on their part. They reckon the country has gone to pot and needs a strong uniting force to return it to what it once was, which again is rather admirable. They simply aren't the best way of doing so, and are too free and easy with using questionable methods and brute force to do so, and are a bit obsessed with gathering power for themselves. Not evil, just misguided extremists. As for slavers, raiders, and so on, they're just greedy murderous bastards, so if you consider real-life killers or slavers or pirates to be evil, then yes, they are in F3 too.
Gears of War - The entire series pretty much deals with this question as a whole, doesn't it? I'd argue the Locust, and later the Lambent, aren't evil. They're simply dealing with what they see as a threat to their survival and existence, i.e. humanity. The fact that humanity view these enemies in much the same way is the crux of the matter, and we are playing as humans so naturally we'll see things better from humanity's point of view. If the game had been released where you play as Locust, killing humans, we'd see the matter a lot differently. On that note, isn't there a Gears 3 DLC pack where you play a campaign as General RAAM? Or hasn't it been released yet?
Halo - Again, entire series here (including Halo Wars and Reach - shut up, I liked them both, and ODST, okay?), including the expanded universe (books, comics, anime, etc.). No, the Coveant aren't evil. Each individual race has it's own motives and reasons for being part of the Covenant, which would take a lot of time to tell (and so I won't talk about them here). Suffice to say, the closest to evil you'll get with them is the Prophets, and even they aren't evil. The race as a whole are simply decadent, hedonistic and lazy, but otherwise no harm and perfectly decent creatures. The Hierarchs (the three leaders) are pretty much just power hungry, with Truth being the most manipulative and smartest of the three, and the entire Covenant War is his fault anyway after he manipulated the new Brute Chieftan Tartarus to attack Harvest 27 years before the games - when the former Brute leader, Maccabus, was actually pushing for peaceful first contact and getting on well with these 'humans'. As for the Flood, they aren't evil either - they're simply genetically created by the Precursors as a weapon, and the Gravemind is simply trying to propogate the species - perfectly natural. Forerunners aren't evil, as the books show - yes, they fought a war with humanity, but not without justification, and on the whole were a very humanlike species anyway. Finally, the Precursors haven't been given enough background yet to make such a judgement (not until we see the rest of the Forerunner Trilogy, and Halo 4, yet...).
Tom Clancy's H.A.W.X. - Yes, I have this game. Yes, I enjoy it. No, I can't make a judgement, since I haven't yet completed it, and thus don't know enough about the main villain or villains yet.
Project Gotham Racing 4 - It's a racing game. There are no villains. Fool.
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For the record, I also have the two main Kingdom Hearts games, but won't be judging those because quite frankly I've not got enough information. I haven't played any of the other games in the series yet save Chain of Memories, which I've never gotten very far in anyway. And these are simply the games I have for PS2 and Xbox 360. I do have more games, on PC and Nintendo DS, but I have too many to remember by heart, so I won't be adding any more to this here list. Sorry guys .[/small]