Howdy:
Just my opinion :-) I have built several machines and this is what I arrive at:
1) use a low power consumption CPU with integrated graphics. Any i3, i5 or i7 Intel CPU with the "S" suffix should work great...the "S' designates a low power consumption selected/binned CPU...low power = low temp = low fan speed=low noise. In the end whatever cooler and fan you specify, if board controlled, will run slower and quieter. BTW, I use a Intel i7-3770S CPU...waaay more that I need but fun to boast of. Almost soundless with:
2) I like Thermalright's lower profile coolers, like the 120 i or M (the 140 might be a bit better/quieter if you have room). I have not found water cooling necessary but that might be an option.
3) Calculate your power supply wattage requirements (search Newegg for this tool) and buy something a bit more capable and go fan-less. For example, if you calculate you need 300 watts, buy 500 watts. This is to "derate" the supply so that it runs "cooler"/lasts longer = more reliable. Of course, no fan = no noise.
4) Do run a SSD boot/program drive. If you can, go all SSD = no noise. I run WD Raptor HDD's for data storage but If I had the $$$, SSD all the way.
5) I built with Fractal Design's R4. Huge case (I run multiple hard drives), easy to build, great cable routing...comes with two very-quiet-if-run-on-lowest-speed fans. Case side panels are sound dampened with a heavy rubber-like absorber. You might check their smaller cases.
Bottom line, do what you can to go fanless. Low power and non-mechanical/solid state.
Cheers