With respect to audio cables I would go with what kcarlile has suggested. Most of the people on here would tend to agree too. But do get nicely shielded VGA cables if you go the video route for HTPC. Interference on a video cable can cause some static in the picture. Any generic cable for audio will do. For audio I'll still keep my Kimbers though.
For analog you would actually need a miniplug to stereo RCA converter (definitely not a HIFI thing) to get your analog mains to your receiver. Don't worry about the sub output here. Make sure your soundcard outputs the full frequency (which it does without resample) and the receiver will do all your bass management as kcarlile has mentioned.
Dont worry about pre amps. processor, power amps and monoblocks. That is why receivers were made to incoporate all those into one box. Less space, cheaper cost, less cables, less complexity.
With respect to using the SPDIF digital connection to your receiver, bass mgt is also done by the reciever so you do not need to worry about that either. It is usually if you are using computer speakers hooked up to your soundcard will you need to setup bass management through your card software package.
Having both digital and analog connections you can find out which gives you better audio quality. With surround you do not have a choice but use your digital connection to decode for DTS or DD. One thing to note that audio quality for this setup really depends on the quality of music from your source.ie if mp3 file is 94, 128k or 256k etc...
The are other source files which can give you better audio quality such as OGG, WMA, etc. You should ask other people on here which have experience on this stuff.
Based on my earlier comparisons a great CD player with excellent DACs to receiver is "better" sounding than a HTPC audio setup with a receiver.
The benefit to having a HTPC is if your source is mostly digital ie mp3s. It is good for NET radio stations. You also would not need an extra DVD player. It also syncronizes properly with a front projector. Do you happen to have a picture of your setup. If there are any empty white walls Sushi can give a most excellent recommendation.
And yes since your HTPC will mostlikely be away from your audio setup cables may cost you the price of a pair of M3's.
1 pair of 10 feet Kimber 4TC speaker wires for main speakers
1 pair of 25 feet Monster XP speaker wire for surrounds speakers
2 pair of 5 feet Monster XP for biamped centre speakers
2 pairs of 5 feet VandenHul D102 interconnects for CD player and main amp
1 pair of 3 feet Audioquest Sidewinders interconnects for centre amp
6 feet Radio Shack Digital coax cable
25 feet generic computer 25 pin monitor cable to projector
Was it worth it? Well....I could have gotten a brand new M60 for all those wires
