I can think of some obvious examples to start with, but my subtle but insidious nominee is Fable III. Fittingly for a pretentious grifter like Molyneux, the game requires you to raise a specific amount of gold or your kingdom is destroyed and you get a bad ending. The goalposts are moved by the game if you raise money in ways it doesn't approve of, and it is simply impossible to reach the fundraising goal in any way that isn't at least Enlightened Centrist levels of evil, the kind that lanyard-wearing neoliberals giggle about. That's right, you need to be at least this evil or your kingdom is destroyed. So deep and really makes you think about the hard decisions that are made by the ruling class, doesn't it? :zizek:
The way the Batarians have been portrayed, from the very start, has always rubbed me the wrong way. Shepard, who is portrayed as a force for good (even his Renegade path has him framed as "crude but effective"), derisively tries to justify the Batarians being outcasts when talking with a terrorist leader speaking about their grievances. Even the goody-goody Paragon options doesn't have anything to convey sympathy. Then comes Mass Effect 2 where Zaeed, the veteran of a fucking PMC, is portrayed as having a moral compass since he refused to let Batarians ("Goddamn Terrorists") join the Blue Suns when he lead them (as opposed to his greedy partner). They're so obviously a stand-in for [designated bad guy in the global periphery], even incorporating some of the DPRK (being a "Hermit Kingdom" and all).
Also, another thing about ME is that class conflict seems to never be brought to the forefront, despite the Galaxy being a crapsacharine neoliberal hellhole where corporations and their mercenary companies run amok, and poverty is still an everpresent problem. It's effort to be a "dark" science fiction setting just end up making it Capitalist Realist as fuck.
Honestly replaying the series with the Legendary Edition has been kind of an eye opener when it comes to just now much of a neoliberal hellhole that universe is, didn't give it much thought as a kid. The Batarian thing always threw me just because it's like they sat down with the intention to design a race for you to hate.
Now that I think about it, the reason it was shocking to me (and maybe to you as well) was because it felt out of place with the socially Liberal tone of the series. If it were consistent, it would have at least made the "government, not the people" distinction but no, mask off. At least they sorta get treated like people by Mass Effect 3.