All,
I spent well over an hour this evening comparing the Wadia iTransport and Onkyo ND-S1's coaxial digital outputs (using the stock power supplies, as well as the SLA battery power from the Red Wine Audio Isabellina HPA):
Source - iPhone using Apple Lossless files.
Amp/Dac - Isabellina HPA
Headphones - HD800s with ALO Audio cabling.
Sound
In terms of sound quality - they are really so close that I really cannot call one a winner.
When using the their stock SMPS adapters, they sound nearly identical.
When fed from the SLA battery power, they both showed an equally noticeable improvement in sound (better defined bass, larger soundstage, better imaging, more extended top-end with less stridency)... what you typically hear when move up to a higher quality digital transport.
I am guessing (just from listening) that they are using very similar circuitry inside (haven't had the time to open them both up and compare)...
Features
Wadia iTransport offers a more solid feel and nice rubber isolation feet. The Wadia also comes with different iPod dock adapters to use with various iPod models (e.g. iPhone, iPod Classic, Nano, etc.).
The Onkyo does not seem to come with different iPod dock adapters, but it has a sliding door on the top to protect the dock plug

The Onkyo has both coax and optical outputs (Wadia only has coax), as well as a USB input. Using the iPod/PC button, you can switch between using your iPods digital output, or feeding the Onkyo from your computer's USB port (thus making it a USB-to-SPDIF converter). The USB input is also nice so you can sync your iPod to iTunes while it is in the dock (Wadia does not have this). The Onkyo also has an On/Standby switch, while the Wadia has no power switch.
The Wadia has analog outputs (what is the point? You buy this for the digital output so you can feed your higher quality dac!) and s-video, while the Onkyo has no analog output and composite video. I really can care less about analog audio or video outputs for these units - but I thought I'd mention it.
Both units come with remotes with basic playback features - nothing special.
Build quality
The Wadia is more solid and feels twice as heavy, but it is also larger. The Onkyo is less than half the height and less deep (and approx. the same width).
Value
Have to give the win to the Onkyo - more features, less cost.
I'm not sure when the Onkyo is coming to North America, but my guess is the price will be
at least $150 less than the Wadia (MSRP = $379).
I hope this has been helpful, and I look forward to reading others impressions and comparisons between these two units.
Best regards,
Vinnie