Best HTPC setup

As far as HDHomerun, yes, you should have some type of antenna with coax running from the antenna to HDHomerun. IIRC, there is a HDHomerun that can capture QAM (the unencrypted HD signal on a cable companies coax).

As far as what direction you want to go in... obviously, that's ultimately up to you.. but for starters, what exactly do you want it to do? Do you want this to sit in a nice unit or are looks unimportant? What about noise? What kind of media sources do you plan to use?