The component input-output aspect of my new home theater system is going to be much simpler than I imagined, and immediately address two of my concerns: that I only have to change input in one place instead of two, and that I can leave music playing with the TV off. That's because the recommended approach the Geek Squad folks suggested is based on a receiver that can take 4 HDMI inputs and offers an HDMI output. Thus, I don't use the TV's input switching at all. All my main HD components (DISH DVR, PS3, HD-DVD, and D-Link) feed via HDMI to the receiver, and then one HDMI cable goes from the receiver to the TV, and I leave the TV always on that one input. Easy-peasy!
The Geek Squad recommended a Pioneer 1018, but after looking around online, I found that its advantages over the Onkyo TX-SR606 are mostly that Best Buy carries it, and its video upconversion is better -- which is not an issue for me since all my inputs are already HD. (Well, I do still have an old VCR in the system, but I haven't turned it on in two or three years, so it hardly is a concern if its upconversion isn't great. And if it is really bad, I could just keep it feeding into the TV instead of the sound system.) On the downside, and this is a big downside, it has only 3 HDMI inputs, plus it costs about $200 more. So I've settled on the Onkyo TX-SR606 which has enough HDMI inputs and whose only real downside, according to C-Net's review, is poor upconversion I would never use anyway.
Rather than adding a remote to my pile this will only replace one since I won't need the TV's remote anymore. (I only use it now for changing inputs, on/off which my DISH DVR remote can do, and volume/mute which the receiver's remote will do.) I even verified I can get a second remote for it for a fair price.
Speakers will be two tower speakers at the front on either side (this will necessitate a little rearranging of the room, but that'll be no problem, I can already see how I'll probably do it), for strong sound for movies and music; a center speaker, which I'll need to put on a shelf behind the TV; and two bookshelf speakers to the rear. Those could be towers too, for better music quality, but it's probably not worth the extra few hundred bucks for movies. Still, I'll look at tower speaker prices and sound and consider the possibility.
I had considered going with a wireless transmitter for rear speakers, but I'd still have to run power cables to them which would be just as messy and ugly. Instead, speaker cables won't be that hard after all. One of them will go on the bookshelves, so the wire will be hidden behind those shelves. The other will go on a shelf over the closet, so I can easily run the wire inside the closet, with no worry about avoiding radiant heating pipes or in-wall wiring.
Adding in the price of cables, a second remote, and shelving, plus the consult I just got, and allowing for some slop factor, I still come in at about three fourths of my original estimates. So I'm pleased with the price and with the results I expect. I can't wait. In fact I'm itching to go out and start shopping right now. And while I originally budgeted this for next month the money is already in the budget so we might go up to Best Buy this weekend and start listening to speakers.