If you got a decent (yet not enormous) amount of cash to spend, you should look at the Logitech Z680 speaker system. It has all the inputs you need - SPDIF optical and coax, 6-channel analog and line-in, and it supports stereo, stereo x2, analog 5.1 (for PCs), Dolby Digital decoding, DTS decoding and Dolby Prologic2 as well. Everything you need in one stylish package.
Also, the sub isn't the weedy little thing one usually finds in consumer home theatre stuff, the amp for just the sub is 188W and the woofer is an 8-inch long-throw unit that handles quite a bit of volume I must say (I've made stuff previously lying on my computer desk rattle down to the floor with it). Ported bass speakers often have these annoying port "breathing" sound artefacts when large volumes of air moves through the channel, but the Logitech unit however has a very large-diameter, U-shaped port to counter that.
This system is awesome; excellent price/performance, good build quality and the physical design is nice. One little drawback is perhaps that it encourages playing games with the bass turned all the way up, thus putting your contract at risk when the neighbors in the apartement nextdoor starts to complain to the landlord.