Mr. Parrot has it right.
Some things to consider:
1. You can run your equipment through the receiver. Some receivers on occasion have some HDMI hiccups, which can vary from receivers. In most cases, that would be the ideal way to do it.
2. HD quality sound is not the proper term, and I say that not to insult you, but to inform you.
Audio can be analog or digital.
It can also be mono, stereo, or a flavor of surround sound, such as 5.1. If 5.1 is available, it adds to the overall experience of watching television or a movie, and for this reason, if you have the equipment, we try to get that feature used in as many applications as possible.
Here's how I would set this up, and again, this is open to speculation, disagreement or discussion.
Sony Blu-Ray to Onkyo
Sony Upconverting DVD to Onkyo
Comcast DVR to Onkyo (some DVRs experience issues, in which case, hook it up to the television)
Onkyo to Samsung LN52A650
As far as the Wii, from what I know, component cables will be your best bet because (as some Wii experts may be able to confirm or deny) that the Wii doesn't have HDMI, and has a standard definition output. I don't own one, and honestly haven't played with them, but that's the best information I have at the moment.
If it does support surround sound (something I also don't know), then you may want to hook it up to your Onkyo for that purpose. You can also hook it up to your TV, but since you'll be behind your Onkyo setting it up and you'll get better sound overall and probably a better ease of use.
Keep me posted, and I hope there are some Wii people out there who can clarify a few things.