Evangelion - Asuka plays Sega Saturn a few times during the show. The fact that Sega sponsored the show probably helped that along a bit.
GTO manga - Quite a few accurate references are made to Playstation games (RE2, FF7, Parappa)...there's even one panel depicting a 'screenshot' from Parappa. One character has a PSX in his room, and he and Onizuka have a go on it. Also, there are a bunch of arcade games that seem like parodies of existing ones, Tekken especially.
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