If you have 5.1 you are also going to want Dolby Digital EX and DTS ES to fully make use of it. It makes a huge difference in movies. The EAX on creative cards along with 5.1 makes a huge difference in games. Most sound cards can also process stereo music out to all channels making it simply sound better.
Most of all you just can't beat the bass, most 5.1 systems come with some high quality woofers that make games and movies all the more realistic and intense.
But I have a 2.1 sound system that uses a stereo connection: It separates it's own sub frequencies from the stereo signal, and that works just fine!
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Both 5.1 DD and DTS has an actual independent subwoofer channel that is as "real" as any of the other 5 channels.
Some people are confused by the term "limited bandwidth" that gets applied to the subwoofer channel. Its not low bitrate, it just means it range includeds base tones.
There is usually no 2.1, 3.1, 4.1 audio output, just 2.1, 3.1, 4.1 speakers. The base is simply redirected from the satelites to the subwoofer based on frequency.
If you are watching something with DD or DTS on non 5.1 speakers, the subwoofer channel gets blended into the front channels then redirected to the subwoofer.
Its true that lower frequencies are harder to pinpoint, but a lot of what gets redirected when you use "small" speakers is very directional, so normal people can notice this redirection,
Also merging and redirecting affects the quality of the subwoofer channel, but that is hard for most people to notice. (I can't).
I use "large" front speakers (with good subwoofers) and "medium" rear speakers.
My reciever knows the range of my speakers, so in theory only the lowest frequencies from the rear channel would get redirected to the subwoofer.
In practice DD and DTS is mastered with the assumption you are using at best large front speakers and medium sized surround speakers.
So when watching something 5.1 my subwoofer only outputs sounds from the ".1" channel.
Actually at night out of concern for my neighbors I turn off the subwoofer and my Reciever redirects the subwoofer channel to my front speakers. I barely notice, except I can not longer "feel" explosions, dinosaurs walking ect.