How does Penumbra compare to Amnesia?

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There's no real reason to compare them as both are excellent games and I highly recommend that you play it. You might find Penumbra: Overture's production values to be a little low but you will hardly notice it and Penumbra: Black Plague is completely on par with Amnesia IMO. Anyway, the game is still brutally scary even if Amnesia is scarier and I guarantee you will be nervous the entire time (even when not playing it).