Yamaha SP-7800
I own this exact speaker set. The main towers do a pretty good job in my system. The center-channel speaker was a bit anemic for the level of sound that needs to come out in a good home theatre, so I put back in the Bose (yes, yes, I know) center-channel that I had before. The Yamaha surrounds are perfectly adequate. I don't use the sub that came with the Yamaha system, because I have a powered subwoofer table that a friend built for me, that outperforms the Yamaha by an order of magnitude.
I second what others have been saying about just using a an A/V receiver to do your switching for you. I use a Harman/Kardon AVR247 (Dual HDMI, XM-ready, iPod-dock ready, 7.1- or 5.1-and-secondary-zone capable).
HD-DVD and Blu-Ray go into the AVR via HDMI. HD cable box goes via component cables and coax digital audio (the AVR supports optical and coax for digital audio) We have the H/K Bridge iPod dock, which is pretty nice. AVR to TV via HDMI, 1080p.
For complex systems, I can't recommend the Logitech Harmony series of universal remotes highly enough. I have one, and it replaced the TV, Cable, AVR, HD-DVD, and Blu-Ray remotes. It allows you to set up "activites" like "Watch a Blu-Ray movie", and automagically makes sure that the AVR, BD player, and TV are on, and that the AVR and TV have the right inputs selected, then switches itself into "all of my buttons except volume control the BD player, volume controls the AVR" mode. (All of the activities are fully configurable through your PC; the remote connects to it via USB for programming). It tracks what components are on, and when you switch activities, it powers off the things that you're not going to be using, turns on the things you will, and leaves alone anything (like the AVR) that were already on, then switches everything's inputs to fit the new activity.
With a universal remote like the Harmony, you don't even really need to worry about which how everything is connected (for instance, if you have 3 HDMI sources, and your TV has 2 HDMI in, and your AVR has 2 HDMI in). You can put two of the inputs into the AVR, put the AVR and the other source into the TV, and run the audio from the third source into the AVR via optical or coax, and tell the remote "for sources 1 and two, TV gets video from AVR, and AVR gets video and audio from HDMI 1/2 respectively. For source 3, TV gets video from secondary HDMI, and AVR gets audio from optical/coax." The remote noodles it all out when you select various activities.
-BP