These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Broken Base: There are many fans who absolutely hate the changes wrought by From the Ashes and do not consider it canon, or otherwise dislike other parts of the setting, such as Expedition to the Barrier Peaks.
As D&D itself suffers increasing fragmentation, the debates between Greyhawk purists begin to seem insignificant. (What did or did not happen 20 years ago in an imaginary world is Serious Business!)
Complete Monster: The aptly named Iuz The Evil, the cambion child of the demon lord Graz'zt and the human witch Iggwilv. In his early career, Iuz rallied an army and launched a series of brutal campaigns that gave him the name 'Lord Of Pain'; that or the atrocities he committed on innocents. Eventually, Iuz gathered powerful sorcerers and drained them of life to add their powers to his in a path to godhood. Eventually becoming a demigod, Iuz ended up feared by all those who knew him, with no care towards either of his parents or any in his way. He eventually resorted to killing his formerly loyal servants and replacing them with Fiends solely for convenience and power.
Evil Is Sexy: Graz'zt, Iggwilv, Eclavdra. Maybe Mordenkainen if you go for older guys. (Although Mordenkainen isn't really evil; he just does evil things sometimes.)
Fanon Discontinuity: Many fans hate From The Ashes, as mentioned above. Name something that's set in Greyhawk after Gary Gygax left TSR and you'll find someone that hates it and doesn't consider it canon.
True Neutral: In earlier Greyhawk stories and adventures, a lot of emphasis was placed on some characters' obsession with preserving the balance, especially the archmage Mordenkainen.
For that matter, the fact that the Scarlet Brotherhood, a racist faction determined that their particular race of humanity must rule the earth, are essentially Aryans is a little cringe-inducing for some.
And, well, the fact that black-skinned elves are... Always Chaotic Evil... has drawn ire from certain quarters. Phil Foglio once provided a humorous Lampshade Hanging of the fact in What's New?