This is not really a tweakers site.
I suggest to start with MC itself. It does have a couple of audiophile options like memory playback, different driver (DS, WASAPI, Kernel)
http://www.thewelltemperedcomputer.com/SW/Players/MC14/MC14_audio.htmCics
The assumption is that lowering the electrical activity inside a PC improves sound quality.
RFI. EMI, ripples on the power rails are supposed to have a negative effect on sound quality.
Now DA conversion is a bit of a vulnerable process.
One might argue if sound quality decreases with increasing system load this is pretty much like having your screen starts to blur with increasing system load so a pretty severe design flaw.
One might also argue that if DA conversion is so vulnerable, one better moves it out of the box into a outboard DAC.
Under clocking does affect the RFI. It will be moved to a lower frequency and will become more dense (the harmonics). But will this improve sound quality or will it become worse?
Nobody can tell.
A low latency is needed to avoid drop outs. We talk a multi tasking OS, not a real time OS so we must remain below a certain threshold. I doubt if low latency for the sake of low latency makes sense. All I/O is buffered by design.
Anyway, do a latency check won't harm you.
http://www.thesycon.com/deu/latency_check.shtmlPower.
Some claim an improvement when running on battery power.
Indeed switching to battery power can make a difference, the power saving schema of you PC can have some very nasty side effects!
An RMAA test will tell you:
http://www.thewelltemperedcomputer.com/SW/AudioTools/TroubleShooting.htmSystem services most of the time do something at start up and than go to sleep.
One might wonder if disabling them really helps.
Disabling drivers in general don't shut of components, they remain powered.
Anyway if you want to fool around with drivers the Blackviper is the ultimate source.
The forum for tweaking PCs for audio:
http://www.audioasylum.com/cgi/etv.mpl?forum=pcaudio