Cracked it, without Audio Hijack. 1. Install SoundFlower. 2. In Audio/MIDI Setup, create an aggregate device (the "+" button) containing SoundFlower and your input device. 3. Launch Soundflowerbed, select your main output under "Soundflower (2ch)". 4. Set Skype to output to Soundflower (2ch) (leave the input as-is). 5. In Logic/Live/GarageBand, set the input to the aggregate device. Create 2 stereo channels, and make a test call.
Now that I knew what to look for, I found that someone already figured this out.
This should also work for Google Talk or Gizmo5 or any other VoIP app where you can set the audio output. In fact, if you set your default audio output in Audio/MIDI Setup to Soundflower, that should make everything else just work.
