I don't think evil really triumphed at the end of TLOU.

What Joel did was awful, but he didn't do it out of malice. Instead he was fueled by a warped need to protect Ellie above everything else, a need the game did a good job of setting up. Would make for great discussion though. Is evil in the action or the motivation? 

He chose to save her over a chance to save the world, and killed multiple innocent people in the process (such as the surgeon). The fireflies couldn't be considered entirely good, but their intentions were. He then lied to Ellie about it, knowing that she'd have rather died if there was a chance it could help. I think that's all pretty awful. 

That said, the game did leave me feeling the same way as you, which shows how good a job they did of justifying his actions. He lost his daughter to those who were supposed to protect, and spent decades surviving it a broken world that couldn't care less about him. Then, when he finally finds someone to fill to space left by what he'd lost, he's asked to give them up. Bugger the world, i'll take Ellie :p 

Every military shooter where 'Murica wins.

The Darkness II
Silent Hill II
Final Fantasy XIII-2
Catherine

That's all I can think of right now.

But 'Murica has to win for freedom! MURICA

For anyone who wants to play an evil character, I suggest BioWare's Star Wars: The Old Republic. Yes, it's an MMO, but where the game shines, for me, is the leveling up process. I basically played it as a single-player game. It's pretty fantastic until you get to the standard MMO "end game" at the level cap. I played a Bounty Hunter as a "for the money" type on the Imperial side, an Imperial Agent who was generally good, and a completely evil Sith Inquisitor. I had a blast with all of them, as all sides have supported choices through-out, even from the very beginning. Playing as a back-stabbing and ruthless Sith Inquisitor was awesome.

Ellie was taken away, Joel had no moment to say goodbye to her and Fireflies were pretty much fixated on taking her life to make a cure. What Joel did, from the main protagonist standpoint, isn't awful. It isn't evil, either. It was just his choice.

You can't say "innocent people" without big quotation marks on it because as far as we know, Joel may had killed innocent people in the past that only fought for survival (You don't get this sense because it's kill or be killed, but just like Joel, there's others with less luck). Mankind is pretty much condemned at that point. Erasing the possibility of a cure only ensures that tickers will still be around, but having a cure does not ensure that society would come back. More like power into the Fireflies hands, if you want to look at it from a crude point of view.

There's a choice to be had, and neither Joel nor Ellie had something to do with it. It was forced upon them. Thing is, Joel simply didn't agree with it; whereas Ellie couldn't say anything on the matter at that moment. Joel also forced a choice on Ellie, but she pretty much stood with him.

Any game that allows for good or bad choices to be made. ;)

Metal Gear and Kingdom Hearts are series dedicated to having the villains win in the end making the heroes work deconstruct around them. Every effort to defeat the villain is just another step in their grand scheme.

Not really. You can make bad choices in Dragon's Dogma, but ultimately, neither good nor evil wins. You can also be evil in games like Dark Souls, but just like Dragon's Dogma, there's no "evil" nor "good" conclussion to the game. A less criptic example would be Metro: Last Light, which allows Artyom to be an evil individual but yet, the game's finale doesn't reflect upon that.