Voadam said:
Both have lots of drow as bad guys.
Both have Drow, yes, but there's a difference in frequency. Largely through the popularity of the Drizz't books, Drow seem to be a dime a dozen in FR. In GH, they're considerably less prevalent in the source material and modules.
There may be superficial similarities between the settings, but after you scratch the surface, you begin to see how they differ pretty quickly. For example, Waterdeep is a true metopolis of enormous size (I can't even remember how big it is). Greyhawk is a more medival-style metropolis of 69,000, swollen by war refugees (that's how it got bigger in 3E compared to earlier editions, it absorbed refugees from the Greyhawk Wars). Wizards generally rule Waterdeep, Greyhawk is ruled by thieves. And so on.
FR may have the Harpers as a secretive cabal of do-gooders. GH has the Circle of Eight as a major secret society, but dedicated more to neutrality and stability than to specifically countering evil.
They may both have pantheons that are hodge-podges of overlapping gods, but in GH, overlapping gods may be from different human cultures and have subtle differences with each other. FR doesn't seem to have much of that.
Zagyg may be a nutball wizard (now demigod) who created a strange dungeon like the Undermountain thing, but as far as most players are concerned, that dungeon might as well by mythical. Aside from Gygax's writings about it as an early testing ground for the game, nobody except him and Rob Kuntz has anything on it. It's almost an urban legend of gaming. Everyone knows about it, knows stories about it, has never experienced it. As such, I really don't consider it a significant correlate with FR any more than any other individual DM's dungeons within GH.
The way I see it, there may be these superficial similarities, but it's the distinctions in the details that have us preferring one setting over the other.