John Falcone, home theater editor Live!

If you're pulling in an OTA signal, the TV will probably send the 5.1 sound to a receiver. If the TV signal is first going to a satellite or cable box (what I thought you were originally referring to), I'd suggest going straight from the box to the receiver instead (for audio).

Our rule of thumb is pretty much this: generic cables are generally fine for short audio and video runs (less than 6 feet/2 meters), but it's often worth stepping up to premium cables for longer runs (in-wall, to projectors, etc.), or if you want to future-proof your AV system beyond any reasonable doubt (for future higher bandwidth video signals, such as 60 or 120Hz 1080p video). You might want to check out a recent Monster Cable story over at Gizmodo, which adds some more detail to this debate:

http://gizmodo.com/gadgets/hdmi-cable-battlemodo/the-truth-about-monster-cable-part-2-268788.php

Using a multi-zone AV receiver (such as the Yamaha) is one way to get multi-room sound in a home, but control and amplification issues could be a real challenge. One "hack" you might consider is going with a Sonos Digital Audio system:
http://reviews.cnet.com/digital-audio-receivers-dars/sonos-digital-music-system/4505-6470_7-32456945.html?tag=lst

That might help address your need to get multiple audio streams throughout the house (though you won't have total control over the non-Sonos components).

As for speakers: We've never officially tested them, but I've always heard good things about the Polk in-walls.

It's certainly possible to mix and match different sizes and brands of speakers, but using matching loudspeakers is generally preferred. As for the woofers--if they're truly subwoofer replacements, you can get away without a dedicated sub. That's the idea, for instance, w/ this Aperion setup:

http://reviews.cnet.com/surround-speaker-systems/aperion-intimus-533-pt/4505-7868_7-31829150.html

HD DVD players remain limited to Toshiba, while only mass market manufacturers--Samsung, Sony, Panasonic, LG--are doing Blu-ray. I think the upscale brands are awaiting a winner in the format war before they jump in. BTW, we've reviewed almost every Blu-ray / HD DVD player released to date:

http://reviews.cnet.com/4323-6531_7-6575534.html

Thanks for clarifying, p2p. Yes, if your TV is using its internal HD tuner, it *should* output 5.1 (Dolby Digital Surround) to an external AV receiver.

The options for wireless rear speakers have really exploded in recent months. Next week, we'll be posting our review of the KEF wireless system--it works great, but it's $600. But we'll also be looking at the Rocketfish ($100) rear speaker wireless system in July. Also, almost every HTIB manufacturer now offers a proprietary add-on for their respective systems, so if you have a recent Sony/Panasonic/Samsung/etc. home theater system, you might want to check for compatible wireless accessories.

One caveat, though: these all do a great job of eliminating the front-to-back speaker wires, but need additional wiring and power in the back of the room in order to work.

Using old receivers to amp up the sound in additional rooms works well, but another big challenge with multi-room setups is remote control access, source switching, and source control. It's fairly easy to get music throughout the house--but if you want to change CDs, switch to satellite radio, and so forth, you'll probably need an advanced RF remote system, at the very least--or you'll be stuck heading back to the main room to change things.

... quite honestly, I don't have enough experience with them to recommend one brand over another. Sorry.