Not oc'ing a 4930K? Oh the horror! ;D You should, it's easy, extra performance for free, and with a rig like that you already have the ideal setup to support it. If you don't want to increase noise then you could limit it to stock-voltage oc'ing or just something minimal (for a 3930K that would be about 4.5 to 4.6GHz, but for a 4930K I guess more like 4.3GHz).
Anyway, yes the same types of fan ought to be fine for other cooling duties, but I shouldn't comment further on water-cooled GPUs as that's not something I've ever tried.
As for the case fans, what model is the case? Some stock case fans are also kinda loud, so again I generally replace them with NDS versions (though if I can eventually get hold of the staggeringly enormous NDS 6 case then I wouldn't have to do that).
I recommend against removing one of your fans, best to have an inflow at the front, though whether you'd want the side to be intake or exhaust will vary depending on the GPU config, etc. You can always run tests to determine which is more effective. For a single 980 Ti I'd normally set the side fan to be an exhaust.
This leads on to the -ve/+ve thing; you'll find raging debates about this on forums, all tied up with dust prevention and other issues. It will tend to be specific to each build as to which is best, but sometimes it definitely doesn't function the way one might expect, and you may find that heat issues are more imortant than dust prevention, though case filters can help there (OTOH, some case filters can add to noise).
In my fairly typical single-GPU 3930K setup (Antec 302 case, one 980), namely the system I referred to above, I have the front as an intake, the top as an intake, the side as an exhaust and the back holds the H80 with two NDS 120s as exhausts, thus the H80 gets fresh air straight from the top intake, while the 980 gets air from the front and kicks some out the side. Al the fans are NDS 120mm PWM.
In a different example though, the above general flow direction didn't work that well so I had to experiment more, namely a 3930K/4.7 in a larger Aerocool XPredator case with four overclocked 900MHz heat-pumping 3GB GTX 580s, the CPU cooled with a partially external H110. See:
http://www.sgidepot.co.uk/misc/3930K_quad580_13.jpg
This time, because the 580s both generate a lot of heat but also need a lot of fresh air, the side panel has
four NDS intake fans, the front fan is a single large Bitfenix Spectre Pro 230mm exhaust, the H110 at the top uses four NDS 140mm PWMs as intakes, and the rear is an exhaust 140mm PWM (actually a Noctua, bought before I discovered NDS).
One might think that the H110 would be better running its fans as exhausts; I tried this, but temps were several degrees higher. I also tried the front fan as an intake, the sides as exhausts, various combinations. In the end, the above somewhat counter-intuitive setup worked best (rarely would a front fan be better run as an exhaust). One thing though, this system wasn't really built for optimal noise, more for best temps and max heat reduction, the big issue being to help prevent the heat from the 580s affecting the rest of the system. The rear exhaust does have a hefty workload to cope with I guess, but it works ok, and the front exhaust can move a lot of air (150cfm).
Two other points of interest: the H110 with four fans uses a 5-way Akasa PWM splitter cable, with power provided by a SATA connector, so that the PWM signal from the mbd drives all four fans at the same speed, which helps ensure there is minimal discordant noise from mismatched fan speeds. Likewise, the side panel intake fans are grouped into two horizontal groups of two, each group linked to a different mbd PWM fan header (I used extension cables so the panel can be removed without having to reach down to the mbd sockets). They are setup so that the upper fan group runs on a more aggressive cooling profile, providing extra air for the mbd chipset area.
And since you're in the UK (hello there!), the NDS fans are on eBay (eg. see item 111585390937), but I bought mine from Scan because the qty I ordered (ten) meant, with the shipping added on, it was cheaper overall:
http://www.scan.co.uk/products/120mm-nanoxia-deep-silence-pwm-ultra-quiet-pc-fan-650-1500-rpm
In the past though I've bought them from specialtech.co.uk and a couple of other places.
[EDIT: Scan has dropped the price by 1 UKP since I bought my batch of ten a couple of weeks ago]
Ian.
PS. What mbd are you using?
PPS. Full quad-580 pics archive (the first six pics were taken when the parts were in a smaller HAF 932 case with very different fans):
http://www.sgidepot.co.uk/misc/3930K_quad580.zip
and OC'ing hasn't really appealed to me yet, but thanks so much for the help! Think you can give any more info since I've just updated my question lol
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