You can keep that butt ugly HAF X and still keep it "silent".

I tend to keep away from "noise muffling" cases as you should be stopping noise from the source, not bandaiding it.

So water coolants for the gpu and cpu?

I've turned the top and side fans of the haf x to a minimum. Decent airflow still, but there's hardly anything in between the gpu and me so I can still hear it quite loudly.

What's wrong with noise muffling? I get that you'd want to optimize other things first, for a relatively hot running setup, but I keep my apartment pretty cool and don't do overclocking, so I think I'd be just fine with a bit of dampening material here and there instead of annoying static fan noise.

The Fractal and Nanoxia cases are reasonably quiet, but the airflow is pretty pitiful. If the GPU has to crank its fans up to compensate for the lack of incoming air, then it's just self defeating. What you want is a case that's got good airflow AND is quiet, like say the new Silverstone RV/FT05. I don't particularly like the design or the uber cheap construction, but it does work.

I also suspect the fans used in the HAF (assuming they are stock) are a major part of the problem. You can't just turn any old fan down to the minimum speed and expect it to be quiet. Delta fans at 5V are not quiet. What you need are some Noiseblockers or Scythes on the case.

Watercooling IMO is totally unnecessary, and "silent" water cooling is largely a myth. First of all the radiators are gonna have fans on them, so there's no getting away from fans no matter what you do. And if you go with one of the Asetek closed loop rebadges, it's total luck of the draw on the pump. Some of them are pretty quiet, some of them make a total racket.

If you're not that into overclocking, there's absolutely zero need to water cool the CPU. A stock or near stock CPU can easily be run dead silent with a good Noctua, Prolimatech, BeQuiet, or Thermalright tower cooler. Just turn the fan down, and/or get a good one (see above) for coolers that don't already come with fans.

For the GPU, just stick an Artic Cooling on it. Noise problem solved.

Well if you don't overclock I would change the case and get the new Fractal Define R5, GTX 780 don't heat at all, for the CPU cooler you could get some nice one from noctua or even an hyper 212X, I guess the hyper 212X will be more than enough, I have an cheap i3 with the cheapo Tx3 Evo and the cooler don't need to spind more than 25%.

Power suply tend to be really noisy too, there are some passive ones, although they're expensive, you could get one that don't spin the fan on idle, something like the RM from corsair. HDD may get noisy too, but there isn't a lot that you can do.

Ow, just one more thing, don't use screws to screw the fans on the case, use something like this -> http://www.amazon.co.uk/Akasa-AK-MX003-Siliconized-Rubber-Pins/dp/B003N7YZLC
Although some guys don't think that these rubber pin work, I disagree 

Best way to manage heat and noise from a GPU is to move to a Maxwell architecture.