Hmm, interesting, it sounds like perhaps something interfered with Audio Hijack's ability to record the audio?
There are lots of audio filters that you can use, using a program like Audacity or the like, to remove noise, but they tend to work well on audio where there is a good signal overlain with lots of garbage and the task is to isolate the "good" part, rather than originally corrupted audio, where there really is no good signal.
Once the noise is out, a compressor also really helps -- this is another tool you can use through an app like Audacity, and its function is to reduce the dynamic range (volume) of the audio -- it makes the person's voice sound much more consistent in volume, and this tends to help get rid of any variation in mic sensitivity as the person turns their head orientation with respect to the mic, which tends to be a much greater effect on mics than what you get in real life when they're standing in front of you (so it sounds unnatural, and the compressor helps undo this).
Also one more thing is that you may want to look at the audio spectrum of the recordings... if the noise is a digital artifact, meaning it was created through some kind of software issue between Skype, OS X, and Hijack, it may present at really specific frequencies that you can filter out, leading to a much better sample.
Have you tried a couple of different playback programs to examine the files Hijack made, to make sure you're not just experiencing some kind of codec issue?
Also... I guess there might be some subtleties with Skype and Hijack...
When you look at this:
http://www.blogarithms.com/index.php/archives/2007/12/23/skype-for-interviews/
or particularly this...
http://www.ryangordonproductions.com/ustream/
Is what you did generally in line with what they suggest? I'm not sure you can do anything about it now, but...
