Firstly, you didn't do too badly on your Yamaha for $62 and a 20 minute drive. That 500 watts is 100 watts per channel (possibly at unreasonable distortion, but conservatively 70 wpc at healthier levels -- which ain't too bad, really).
I'll let others comment on the Pioneers and SVS sub. I'll comment on other things.
Firstly, if you end up putting this gear into your living room, get an area rug if you don't have one. Consider it an essential part of your home theater setup.
For a keyboard, the best wireless HTPC keyboard with touchpad is the Rapoo E9180P at the moment. The E9090P is expected to become available this summer and will add inductive charging and backlit keys; but for now, the 9180 is the best for the money. If you aren't a very good touch typist, you might have to look for a Logitech DiNovo Edge, but its touch pad isn't really much of a touch pad.
For a video card,
this fanless Asus GeForce GT610 will handle x264 @ 1080p in silence without breaking a sweat, and it has an HDMI out to carry audio + video from your PC straight to your Yamaha receiver via a single cable.
I'm pretty fond of my Samsung television. If you decide to get a Samsung DLP TV as well, using it as a PC monitor can be a little tricky if you aren't prepared. When you plug the receiver into the TV, make sure you plug it into the "HDMI / DVI" input, and then go through your TV's setup menus to rename the input "PC". It took me a long time and a lot of searching to
make my text readable using my TV as a monitor.
What else? XBMC is free and excellent for organizing your movies and TV shows and browsing from the couch. A Logitech Harmony remote will be great for navigating XBMC, turning on your CD player, and whatever else you want to do; but you'll need an MCE compatible USB IR receiver. (The cheap Streamzap receivers aren't MCE compatible, so you won't be able to make your Harmony do keyboard-ish things that XBMC requires.)
Anyway, good luck!