Hi etotheipi,
I've tested the quality of the "Smartphone -> PC" connection, by playing an WAV file (containing modulated audio at 48 kbps) from a Nexus 5, and recorded it from a PC microphone jack - using a standard 3.5" male-to-male cable. I've successfully demodulated a single 16kB file transmission, containing random binary data.
For the opposite direction, I need a special cable that allows me to connect to the microphone of the smartphone, so I've ordered the following cable, that seems to be fit for the job:
http://www.aliexpress.com/snapshot/6288177801.html.
I will report my results when I get the cable

Regarding smartphone<->PC communication: it's indeed an interesting problem. I'll think on it...
Smartphone <--> Smartphone, too. The nice thing about the audio solution is that there's no reason it wouldn't work, you just need the right cables. And of course an Android version of the audio xfer

Regarding "Smartphone <-> Smartphone":
I think that it may be done easier by some kind of "QR-video" solution, since both of the smartphones should have a camera, and they are quite easy to operate (as compared to desktop screens and webcams). In addition, since we need to achieve ~6kB/s rate, we can use the larger versions of QR codes with quite low fps value. For example the largest version (#40 = 177x177) can contain 2,953 bytes = requiring 2 QR codes per second to achieve the required rate (see
http://www.qrcode.com/en/about/version.html for details). The Android application itself will probably look very much like this one:
http://stephendnicholas.com/archives/310 (which quite cool IMHO).