Is it possible to "pipe" audio into the "line in" for a particular program?
Solution 1:
For Linux, JACK sounds like what you want to do. It's rather confusing, though. The last time I needed to do something like this I gave up on JACK and just set the (system) audio input to the monitor of the output in PulseAudio (Kubuntu).
For anyone wanting to do this on Windows, Virtual Audio Cable does the same thing - and is much more intuitive to use, though that could be my lack of experience with Linux.
Of course, programs like Skype may have their own internal system for doing such a thing and that would be the best to use.
Solution 2:
For linux, I think you'd want to try Jack, but there's a program that does what you want called Soundflower.
Solution 3:
I don't know that there's a way to solve this problem in a very general way, but in any case I've implemented what I wanted for Skype. You can see it here on my GitHub. It allows you to select an audio file and play it into an already active Skype call.