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When Misa sends her fake Kira diary to lure Light to Aoyama, one fake entry reads "Read Jump for the first time in ages. Reading it all in one go was fun." And what magazine originally ran Death Note? Yep. Shonen Jump.
The spin-off novel Another Note: The Los Angeles BB Serial Murder Case has a character make several Fan Boy-ish remarks about Akazukin Chacha. This almost results in a Weird Al Effect of sorts.
In episode 14 of the anime, Light searches somthing in the computer using a site called Gentle!. The site layout and the font colors are a clear reference to Google.
The jumbotron Light passes while walking home is made by "Fanasonic".
In volume 8 of the manga, we have Ide disguised (hopefully unintentionally) as a certain dictator. How this got past most everyone's radar is impressive itself (but after reams of pages dedicated to killing, nasty plots and a god complex, it just isn't that surprising).
I'm surprised this one seems to went unnoticed for so long, but remember that last shot of Light's dead face that takes over the whole page? Go see the last frame of the controversial Caligula movie starring Malcolm McDowell (herefor now) and tell me if they don't look awfully similar.
L's in-person introduction to the considerably slimmed-down task force: "Bang."