Digital Optical and Digital Co-axial have insufficient bandwidth to carry HD audio. HD audio can be output as bitstream (raw data) from the player for external decoding by the amplifier (equipped with suitable HD audio decoding) or it can be decoded internally by the player and output as LPCM. This can be transmitted over HDMI or using the player's DAC, decoded and converted to analogue and output over multi-channel analogue cables. The latter method is used mostly by those folks with older amps that lack HDMI.
Phono carries two channels (stereo) but they're just a single length of cable capable of carrying one channel of audio. In a stereo setup, this is simply left and right but obviously in a multi-channel setup, each length of cable carries a single channel of audio. As I said, using multi-channel phono cables is for people with older amps and those that use SACD and DVD-Audio.
If you're buying new equipment including Bluray (BD) player and AV receiver, they will invariably be equipped with HDMI, so don't worry and obviously when you come to buy, check the reviews and post further questions on the forums.