Covered Up: "99 Problems" was originally a rap by Ice-T.
Within the rock/alternative world, Jay-Z has himself been covered up by Hugo Chakrabongse, who borrowed the same hook for a bluegrass song.
Ear Worm: "I got 99 problems but a bitch ain't one." As well as many of his other songs.
First Installment Wins: His debut Reasonable Doubt is generally considered by critics to be his best album, followed closely by The Blueprint.
Funny Aneurysm Moment: His song "D'Evils" is a fictional account of violent fallout with his friends over Money, Dear Boy. Though no where near as bad as what happened in the song, he did have a falling out with his friend/business partners and some of his artist, resulting in the end of his record label Roc-A-Fella Records.
Nightmare Fuel: The "On To The Next One" video, which involves Jay-Z and the director having fun with all the Illuminati-Free Mason rumors leveled against him, and quite a bit of disturbing imagery. Hell, on it's own, the song isn't exactly something you'd want to listen to in the dark.
Sequelitis: Some feel that the two sequels to The Blueprint don't live up to the original. Hell some think that everything he's made up to this point doesn't compare to Reasonable Doubt
They Changed It, Now It Sucks: Some of the reactions to albums such as In My Lifetime, Kingdom Come, and The Blueprint 3 due to them having a more "pop" sound. In some circles the Blueprint get this as well. Or ALL of Jay-Z's output post Reasonable Doubt.