You may be asking this question in the wrong place. You may get a better answer
at AV forum (
http://www.avforums.com) or AVS forum (
http://www.avsforum.com).
To answer your question as best I can. Including the TV in a TOSLink setup will add an extra decode/encode
stage. This will affect the timing of the audio signal, perhaps degrading the quality of
the signal (there is no timing synchronisation over TOSLink, though receivers/DACs
can compensate). For similar reasons, keep your runs of optical fiber short: 1-2m if possible,
6m as an absolute theoretical maximum.
TOSLink has much higher audio bandwidth than HDMI: 125Mb/s versus 36.86Mb/s. This may
be more significant for multi-channel audio, though, since even 320Kbps should cover your needs.
TOSLink is also completely immune to electrical interference, so you don't need to worry about where
you run the cables.
HDMI will synchronise audio to video, which is better if you're watching movies/TV,
but the audio is not clocked (so you can get "jitter" here too).
Again, keep to short cable runs to avoid video/audio distortion, and minimise the number of
devices in the chain for the best audio experience.
So it's not clear cut. For audio, your best solution is probably TOSLink direct to the DAC/stereo amp, but the other
routes may be completely acceptable (you need to listen to them to see whether you can hear any
effects). For video+audio, use HDMI.
If you want really good sound quality (and can afford it), add a separate DAC. I have my AppleTV 1G
connected through a Cambridge Audio DACMagic to my old stereo amp, and it's great, but this
is audiophile territory! Most people will be happy with a simple TOSLink to amp connection.