Water cooling is in general a LOT quieter. Its more efficent and the fan that goes on the radiator can spin relatively slowly compared to air alone. So for like an HTPC it works great.
I use one on my main machine bu may go back to air on my next one. Why? They require regular maintenence
1) Surprisingly the coolant evaporates
you need to fill it up every few months, and if you forget and it goes below the priming level of the pump.. yow.
2) Mold. You can get some fluid with antibacterial stuff in it or you may have to add it yourself, but you need to keep an eye on your lines and if they start getting cloudy, put new fluid or a new shot of anti-bacterial agent in the fluid quick before it clogs up your radiator.
The maintnence isn't BAD but you DO have to keep a eye on it regularly (just like your car!). But.. boy are they quiet, and if you are using an SSD and enjoy it's silence and want low noise over all from your machine, then water cooling works really well for that. (Can even use on some graphics cards to keep the fan npoise low there too)