Surfing the web, I found a very interesting (now discontinued) IR universal remote device: the Total Remote made by Griffin. This device was used with a Windows Pocket PC and consist of an IR transmitter designed to be put in the headphones connector and a Windows Pocket PC program to capture, learn and re-transmit the IR signals. But how did they do it?
The IR signals are saved as a stereo audio .wav files with two half frequency sine waves out of phase by 180 degrees (one in each channel). In the transmitter each channel are connected to an IR led in such a way so that when the sine wave peaked it would emit a short IR pulse. The result is an IR carrier at twice the max frequency of an audio player (~22 kHz), thanks to oPossum for this explanation :-).
Check out our interpretation (the IR sampler) of oPossum's circuit and PIC software below.
Click on the picture to enlarge it and read our comments and advice