As you move up in feature/price levels for motherboards, you move up in quality for on-board sound. The better motherboards have excellent sound on board and many are designed specifically for integration into home theater applications. You have to remember, in most cases, you are simply moving digital data around just as you would a file - and that is not too hard to do.
The reality is the biggest variable in quality audio reproduction is always the speakers. That's because they are "electro-mechanical" devices. PC speakers are typically amplified - meaning the preamplifiers, converters (if any) and amplifiers are built into the speaker system, typically the sub-woofer. This is all part of the cost of a PC speaker system.
For a real reality check - quality home theater/stereo speakers easily cost many $100s or even $1000s for just one speaker! Plus it costs $100s or $1000s more for the amplifier/receiver electronics. So don't expect audiophile quality sound from a $200 or even $500 set of amplified PC speakers. Yeah, if you're playing a game or watching a DVD, the audio takes on a secondary position in the hierarchy of your attention, but if your goal is serious music listening, you will have to output your audio to quality external electronics (HT receiver or separates) and serious speakers.
Remember, loud does NOT equal quality.
And yes, even the most basic motherboard will have front panel headers to move front left and right outputs and microphone input jacks to the case's front panel for headphone use.