and read often that Asus boards are the best.
Well i would put that Asus is a pretty good motherboard manufacturer, but the best idk, there are different boards from all manufacturers and most are good, it really depends on what you are looking. For my intended purposes Asus for me its the worst, as it has high restrictions on pure bios fan control, i dont like to run extra software to control fans, and in the case for asus to have good control you do need it, at least thats my opinion. There are better option that fit more what im looking, like MSI (and i think AsRock) that have better bios fan control. But i still continue to recommend asus, because even though its not the right fit for me, they do produce good motherboards and for someone looking for an easy quiet setup, Asus + FanXpert works pretty good.
I really would like to avoid anything in software
Look into MSI and AsRock, in certain motherboards they offer 2 PWM fan headers, in MSI is CPU_FAN1 and CPU_FAN2, in AsRock i believe is CPU_FAN and SYS_FAN1 (you have to crosscheck this), but its not on all motherboards you do have to check it for each.
OK thanks. I'm looking at the H87 (microATX)boards at the moment, and they too, seem to be updated with respect to the Z87 boards. The H87 features three true PWM 4-pin fan headers (2 CHA + 1 CPU), in contrast to the Z87 "fake" 4-pin headers. The two CHA headers can be adjusted with a duty cycle between 60-100% and the CPU header from 20-100%.
Asus H87 motherboards will only have 1 true pwm fan header, H97 might have more according to what loadstar have posted, i cant confirm it as i dont own one to say for sure.
It specifically states in the manual that ONLY 4-pin fans can be supported by the fan software. So, with this board, it seems that 3-pin fans would only run at full speed (+12V). To me, this doesn't seem to be a satisfactory answer to keeping your system quiet if you have 3-pin fans. From the manual:
Only 4-pin CPU fans and chassis fans support the ASUS FAN Xpert 2 feature.
Be careful as Asus tends to lies in some aspects, like whats PWM or voltage controlled, thats up to Z87/H87/H81, suppose to change on H97/Z97, but i dont expect it to change, again i dont own recent motherboards to say.
On fanXpert2, on an H87 motherboard, you will be able to control both CPU_FAN (real 4pin PWM) and CHA_FAN (fake 4pin, voltage controlled), its just a matter of loading AI Suite III and run the tunning, then you can adjust the graphs to what you like. But the important thing is to understand how Asus motherboards are design, specially the fan headers, and chose the correct fans for each. CPU_FAN you can go with 4pin PWM (or 3pin fans changing in the bios from AUTO to ADVANCED), on CHA_FAN headers use 3pin fans only.
It would appear then that there's no fancy switch in the header to detect whether to run in voltage- or PWM-mode.
On Asus motherboards, at least that ones that i have owned, there is an option inside the bios called Q-FAN, if its seleceted AUTO = 4pin PWM, if ADVANCE is selected = 3pin voltage control, this was only available on CPU_FAN header on my motherboards, on the new Asus H97/Z97 it seems that this has been implemented to the chassis headers, but i cant confirm this as i dont own one.
As for your comment regarding the y-adapters, my question was geared to running 2 of the same sort of fan to one header, in which case you would need a y-adapter. How would the sensor get its info?
When you use a 4pin PWM fan splitter, one of the ends remain 4pin (current, ground, rpms and PWM), while the other is 3pin (current, ground, and PWM), this means only 1 fan will report the rpms for both, usually works fine as long as you use the same fan on both ends. There are more fancy PWM splitters that draw power from 4pin molex or Sata power, but the principal is the same, only 1 fan reports the rpms, but all get current, ground and pwm singal.
If you are only going to run 2x 120mm PWM fans, and both are the same brand or model, and you want pure bios fan control, no software. Then go with MSI and get PWM fan splitter and run both fans from the CPU_FAN header, enter the bios and set the fan curve. If you want to control each fan individually, search for MSI motherboard with CPU_FAN1 and CPU_FAN2, here a pictures of my setup controlling CPU_FAN1 and CPU_FAN2 headers on pure bios.