imho, upper cage is much better. put a 120mm fan in
front of the cage, and you're good to go. i have two hdds
in the upper cage, and only one in the lower cage. as i
said, there is a papst 120mm fan in front of the two hdds
in the upper cage, and as for the lower cage, the stock
120mm fan which came with the case running at min speed
(which i have put in the opposite direction than as it came
originally with the case - it blows towards the front rather
than to the back of the case).
the hdds in the upper cage, with fan running @ min speed,
go up to 37-39c, but teh hdd in the lower chamber rarely
goes under 39-40c. i can get it as low as 34c with all of the
fans at maximum.

(including cnps9700 on cpu and vf900 on
vga card - the hdds in the upper cage then go as low as 31c,
the vga card goes as low as 34c, chipset @ 37, pwm @ 50-52c,
and cpu as low as 21-23c - but as you can imagine, with all of the
fans running at max, it starts to sound as if you were somewhere
near a waterfall or sumptin).
the vga card itself is running at approximately 39c all of the
time, and that's after i have replaced the original one (before the
replacement the card wouldn't go in idle mode anywhere near
39c - 48c was the best). which means that hdds in the upper
cage ain't really blocking any airflow to the vga card at all. in fact,
my hdd in the lower chamber suffers the most.
the psu is running contantly at around 900rpm. it never goes
beyond that, even when the computer is fairly stressed.
the cpu is not overclocked, and it runs with everything on min
@ around 31-34c.
so, my vote goes for the upper chamber, unless... unless you
have a vga card that heats up like a motherf....r (8800, 2900 etc).
oh, yes. i almost forgot. put some fan controler for the 120mm
fan in front of the upper hdd cage. this way, you can control
the air intake as you wish.
but, also i must say, with two zalmans in the case, a chipset
fan, four 120mm fans and a psu fan... it is quiet, but is not
inaudible as someone said. so, if you gots the dough, maybe
you should try nexus 120mm fans. btw, has anyone tried
replacing the stock fans with nexus ones? do you have a fan
controller or sumptin, because those stock fans can be "excused"
for their noise, for at least you do have some control over their
speed(s).
ps.
forgive me, this is my first post.
