To get the best possible airflow with the least amount of noise, install as many fans in your case as possible. Preferably 140mm rather than 120mm since 140mm fan moves more air and does that more quietly than it's (same spec) 120mm counterpart.
Which translates into:
front - 2x 140mm intake
top - 2x 140mm exhaust
rear - 1x 140mm exhaust
While installing 5x fans in your PC may look like that you'd get extremely loud noise out of your PC, it's actually vice-versa. The trick is that the more fans you have inside the case, the less each fan has to work to maintain the airflow and the less noise fans produce.
And that is also a main reason why i have 7x case fans in my Skylake and Haswell builds. Mostly 140mm but few 120mm as well. Full specs with pics in my sig. Since i have that many case fans, i can keep all of my case fans spinning between 800 - 1100 RPM and thanks to this, my PCs are very quiet while still having proper airflow inside my full-tower ATX cases.
For CPU cooling, i'd go with air cooler because you won't gain any cooling performance if you go with AIO over air cooler since both are cooled by air. (For equal cooling performance between AIOs and air coolers, rad needs to be 240mm or 280mm.)
Here are the positive sides of both CPU cooling methods:
Pros of air coolers:
less cost
less maintenance
less noise
far longer longevity
no leakage risks
doesn't take up case fan slots
additional cooling for the RAM
cools down faster after heavy heat output
Pros of AIOs:
no RAM clearance issues*
no CPU clearance issues
takes longer time to heat up during heavy heat output
* on some cases, top mounted rad can give RAM clearance issues
While how the CPU cooler looks inside the PC depends on a person. Some people prefer to see small AIO pump in the middle of their MoBo with tubing going to the rad while others prefer to see big heatsink with fans in the middle of their MoBo.
Main difference between AIO and air cooler is that with AIO, you'll get more noise at a higher cost while cooling performance remains the same.
Here's also one good article for you to read where king of air coolers (Noctua NH-D15) was put against 5x high-end AIOs, including king of AIOs (NZXT x61 Kraken),
link:
http://www.relaxedtech.com/reviews/noctua/nh-d15-versus-closed-loop-liquid-coolers/1
Since NH-D15 aesthetics isn't best due to the beige/brown coloring of their fans, i usually suggest going with Be Quiet! Dark Rock Pro 3 which has far better aesthetics while cooling performance difference is 1-2 degrees Celsius from NH-D15,
review:
http://www.tomshardware.com/reviews/be-quiet-dark-rock-pro-3-cpu-cooler,4350.html
pcpp:
https://pcpartpicker.com/product/9bFPxr/be-quiet-cpu-cooler-bk019
Personally, i'd go with air coolers every day of the week. With same cooling performance, the pros of air coolers outweigh the pros of AIOs considerably. While, for me, the 3 main pros would be:
1. Less noise.
Since i like my PC to be quiet, i can't stand the loud noise AIO makes. Also, when air gets trapped inside the AIO (some AIOs are more prone to this than others), there's additional noise coming from inside the pump.
2. Longevity.
Cheaper AIOs usually last 2-3 years and high-end ones 4-5 years before you need to replace it. While with air coolers, their life expectancy is basically unlimited. Only thing that can go bad on an air cooler is the fan on it. If the fan dies, your CPU still has cooling in form of a big heatsink. Also, new 120mm or 140mm fan doesn't cost much and it's easy to replace one. While with AIOs, the main thing that usually goes bad is the pump itself. And when that happens, your CPU has no cooling whatsoever. Since you can't replace pump on an AIO, you need to buy whole new AIO to replace the old one out.
3. No leakage risks.
Since there's liquid circling inside the AIO, there is always a risk that your AIO can leak. While it's rare, it has happened. It's well known fact that liquids and electronics don't mix.
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