Best HTPC setup
Well, kid number two turned out to be a lot more expensive (in terms of time and $$) than I had planned so I put this on hold until after I finish grad school.
I was never very happy with where everything stood as far as interoperability, etc... and I hated the idea of being tied to anything.
Still, there are some interesting things rumored... the HDPC-20 from directv which will supposedly allow you to use your media pc to record and control content sounds pretty nice. If it is network capable (like the HDhomerun) I think i would get that, use a media server in my office and then an xbox 360 as an extender.
I'm also looking at some hacks to the AppleTV which might make it more attractive to me, but right now it looks like too much work for me.
As far as guidance... I got most of my research from avsforums.com ... this thread in particular is great:
http://www.avsforum.com/avs-vb/showthread.php?t=940972
Be prepared to have to mess around a lot. It's a lot more stable than it was 3 years ago, but it still isn't at appliance status yet.