Some motherboards come with extra connectors for digital audio, either optical or coaxial. Digital audio can carry several sound channels on a single cable. Even if the motherboard doesn't have a digital connector built in it might come with an extra backplate with connectors on it.
You can still get multi-channel sound with just the Mic/In/Out on some motherboards - my Gigabyte GA7VA for example. There's a utility that lets me assign the Mic socket to be 'rear left + rear right' stereo and the In socket to be 'centre speaker + subwoofer' (I may have the sockets mixed up) with Out remaining 'front left + front right' stereo. It means I exchange the audio-in and mic functionality for surround sound. The connection for my surround sound speakers is three cables ending in mini-jacks.
For certain games, like 3d shooters where you can hear people behind you, surround sound can be great. Most of the time it just adds to the atmospherics though.
A more important consideration for gaming is the performance of your audio hardware. Using surround sound will slow things down a bit, but with a high-performance dedicated sound card the slowdown will be insignificant. For a cheapo sound card the slowdown can be noticeable. As with soundcards, some motherboards have high-performance audio hardware and some have cheapo rubbish. I'm not really into high-performance gaming so I haven't researched which motherboards are good audio performers (speed-wise), but I'm sure I remember seeing an article on
Tom's Hardware that analysed the slowdown for several audio solutions, including motherboards and sound cards.
So the answers are "yes", there are motherboards out there with real 5.1 sound - in fact you'll be hard-pressed to find one without it - and "maybe", it
can make sense to have it enabled for gaming, assuming you have room for six speakers and lots of wires!
Nelviticus