Pen's Nest

Neon. Looooooooots of neon in the background decor (which is of course a TOKYO cliche, not Japanese society at large, but that's where the cliche comes from, so...)

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The food...not just sushi, but the presentation of all their meals is basically phenomenal when compared to the rest of the world. Even schoolchildren and 9-5ers lunches are beautiful arrangements of color, proportion, clean lines, etc.

Baseball as a "national" pastime and other "embracing Western culture" motifs, since these are all elements of modern, post WWII Japan

Pokemon. Its popularity has faded here in America (and in the UK, I imagine, though I'm not sure if it was ever as popular there as it was here), but it still has a retail presence and has become a recognizable part of popular culture for over a decade...I expect that's all the more true in Japan itself, though I don't know if that qualifies it as a "recognizable stereotype"

I'm not familiar with "The Mikado", but if it contains a dark or criminal element, the well-muscled gangster with tattoo sleeves (implication: Yakuza) is certainly well known.