Lots of great points here, although it's a little hard to concentrate on philzgr8's comments
Clearly there is no such thing as the ultimate HTPC - the best HTPC is a compromise of size, power, features, heat, noise and aesthetics to meet the individual's needs. "High-end system without paying stupid premiums" is a good quote - that's roughly how I'm going to start my piece. As philzgr8 says; "Something like a decision tree to see what the user finds important!"...
umm...

... sorry, got distracted again.
I'm trying to keep it under $AU2000 - I haven't decided if that includes the OS. David's point on my blog is a good one; "for now, if you really want your readers to actually use their Media Center - recommend XP MCE". Fighting with Vista is the bit of this job I've been looking forward to the least. Exactly what MCE functionality do I lose if I go with XP rather than Vista? Can someone give me a good reason not to switch to XP?
The other consideration is that I think XP MCE is only available as an OEM - exactly how much gear do you need to buy from a shop before they'll sell you XP MCE. I suspect if you've got a good relationship with your shop/s - as the kind of readers I'm targeting will - you'll be able to sort something out.
I think the first choice people need to make is the case, because just about everything else relies on that. The Zalman HD160 looks good, but I also read good things about the Fusion. I'll mention a few in my review but when it comes to the actual build there can be only one - I'm open to arguments on both sides. atechfabrication.com is just too expensive - like I said, I'll have to ditch the "ultimate" tag
The network storage comment is a good one - the fewer the drives in the HTPC the better.
The graphics card is tricky. Needs to be dual DVI, if not HDMI, with HDCP. I think it also needs to be passively cooled to keep the noise down. I think it needs to be an 8000 - I'm open to suggestions of exact makes and models. Might narrow it down to two or three and try them all.
Keep the suggestions coming. I have to file in July so my goal is to have the box built by June and spend a month fine tuning it.