As far as software goes, there are many, many, many front-ends that will help with your HTPC. I think what Windows 7 has straight out of the box is a great start, though. It has a pretty complete media management suite (Windows Media Center) with which I think you should familiarize yourself before looking to the third-party front-ends. Just get a feel for how this works, and then from there you will get a better understanding of the other solutions out there, and how they all work. Think in terms of learning to walk before running.
I didn't notice this in your specs list, but I think you may consider purchasing an infrared transceiver so that your remote can talk to your computer. There are about a million options for this, too, but a stock Windows 7-compatible setup can usually be had for under $20 shipped, and that's with a remote and transceiver (
try this link as an example). If you have a universal remote, you can just program it to work like the Windows remote, and —
voilą — you can ditch the Windows remote. The transceiver will (most likely) be USB-based and come with a decent wire length, so it can be installed in a discreet way quite easily.