Those who think that only 1st-Person-Shooters face problems with censorship are mistaken. The NES-porting of the ICOM-PC-adventures "Shadowgate", "Déjà Vu" and "Uninvited" (ported in exactly this order) had to be altered when they were realeased on Nintendo's "Toaster" (as some of the fans like to call it).
Comparison between the 1987 PC version of "Déjà Vu" and the censored 1990 NES-version.

The Syringe
In a room in the top floor of Joe's Bar you in the uncensored version can find the (empty) syringe that was used to inject some drugs in the main character's arm.
In the censored version the syringe was replaced by a medicine capsule. Curiously enough, the censors actually didn't pay close attention to the text, thus it still says that something was "injected" into the main character's arm.

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Intro of the NES Version

Alcohol
Several alcoholic beverages were altered in the NES version (e.g. a glass of booze on Joe's bar). In the NES version it's a glass of water.

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The Prostitute
In a dark alley near the police department you run into a woman. After you knocked her out by using your "punch" you in the PC version get to know that she's a hooker.
In the NES version she's no longer a hooker. They also altered all the puns ("...red light"..., "...a hooker who has just been right-hooked...") were altered as well.

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Text / Violence
Several texts and animations have been altered for the NES version.

Examples:

Joey Siegel's Corpse

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Censored Animation

Shooting the Prostitute

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Censored Text

Getting Shot by the Prostitute.

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Censored Text

Entering the Police Department Without Clues.

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Censored Text