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Option 1 with the fans between the radiator and the case.
If you have bottom intake or side panel intakes, definitely option 1.
Option 2 with fans on top. Corsair recommends this.
I have a 550d and I have the fans inside the top of the case then the rad. The fans blow thru the rad down into the case sucking air from out the top.
I don't see why anyone would mount it any differently.
I have a Corsair 500r and a H100 in config 1, doesn't seem to affect the temps much. 2500k @ 4.6ghz 1.325v mid 20's idle, 64 max load running prime95 for hours.
Even though the other config is recommended, I hate dust very much.
With my case the 500r, Corsair says to use the option one you listed but make the rear fan an intake to provide fresh cool air to blow out through the radiator.
I use this config with a magnetic filter on the rear fan to remove dust. the 500r case works and looks amazing with the h100 imho.
I did option 1 since I don't really want to increase the heat in my case. I also have 8 fans running with 1 of them pulling in cool air from the side panel so I get cool air running to the H100 so my temps have been pretty good.
8 fans?! Where do you fit them all? I will only be having my front intake which is 200mm and rear exhaust 120mm with H100 mounted at the top. There is no vent for a side panel fan, I hope I have enough circulation!
2 from the H100, 2 front intake fans, 1 140mm side fan, 1 bottom intake fan, 1 rear exhaust and 1 connected to the hard drive cage fan bracket. It's a pretty cool feature for NZXT to include a tilting fan bracket next to the cage.