HDMI is going to be better. HDMI 1.3 will support advanced audio formats like Dolby TrueHD and DTS-HD, which are hi-res audio formats (24-bit/96kHz). Because of copy-protection, I don't expect these formats will play at full resolution over optical or digi-coax connections. At least DVD-A and SACD have never been allowed over insecure digital connections.
Of course, these new audio formats are only going to be available on HD-DVD / Blu-Ray players and since HDMI 1.3 was just released as a spec there's no real hardware yet. Yet another reason to wait on buying an HD movie player.
In the meantime, I think your setup probably makes the most sense because it's digital and lets your receiver work out the decoding. If you do happen to have (or buy) an HD-DVD or Blu-Ray player prior to HDMI 1.3, check the manual for recommended audio hookup. You might get the best sound out of analog cables unless they let you transcode to full-res PCM over optical. The manual should tell you what gets sent over the digital connections and if it's less than what's on the discs, try analog connections and see if they sweeten the sound.