It depends on which audio signals you are passing. If you own a high definition player capable of decoding and passing high resolution audio from BD or HDDVD then definitely you want to use HDMI. The lossless audio codecs (Dolby TruHD etc.) carry much higher resolution audio signals and cannot pass over coaxial or optical digital cables. Also, if your player allows decoding of DVD audio discs or SACD's then HDMI (depending on the version) will allow you to pass that info to your pre-pro/receiver. Coax or optical digital cables cannot pass this information. It used to require having RCA pre-outs on your DVD/SACD player and connecting them to your pre-pro/receiver. This will save you from having to connect 5 sets of RCA cables from your player to your pre-pro/receiver. If you are just wanting to play the standard Dolby/DTS soundtrack on a DVD, or music from a standard CD, then the only advantage of HDMI over coax or optical is saving one cable.
I prefer using Digital from DVD and CD players to the Receiver as much as possible, mostly because I know that without spending good money on the DVD/CD player, that my Yamaha's DAC's will be a higher quality than the players.
Now, with that being said... Most DVD players that offer SACD out for the receiver should have fairly decent DAC's (unless I'm mistaken and some other, cheaper devices are on the market).
I do agree that HDMI would be better than the analog SACD out... if only to keep all processing in the same device.
Having decoded to 5.1 linear PCM sent to the AVR/Pre-Pro has the advantage of letting it do DSP processing of the audio for room equalization, bass management, applying Dolby PLIIx to drive 7.1 rear surrounds, etc.
Legacy digital interface, S/PDIF, over coax or Toslink is limited to 2 channel linear PCM only, or lossy 5.1 DD or lossy 5.1 dts. This is because that is all the content providers would allow (policy decision -- not a bandwidth decision) since S/PDIF has no copy protection (encryption) mechanism unlike what the HDCP that HDMI 1.0, 1.1, 1.2a or 1.3 does have.
HDMI 1.3 will allow the new advanced audio codec's raw bitstream to be transported. So your later this year when they become available, uber new AVR/Pre-Pro, can then use its 7.1 lossy DD+ or dts-HD HR decoders. Or better yet 7.1 lossless Dolby TrueHD or dts-HD MA decoders. Right now BD or HD DVD players must have the new codec decoders built into the player and send out as multichannel linear PCM over HDMI 1.0, 1.1, or 1.2a to the AVR/Pre-Pro. Or as decoded multchannel analog audio with multiple RCA interconnect cables.
I've heard bad and good DACs. Good DACs can make an audible difference. My current attitude towards DACs is I'm only going to pay for them once: in the processor. I'm not going to spend money to buy good DACs in a transport if I've already done that in the processor, and this way all sources get to benefit.