I used Skype for the most recent neRRRdcast and the results have been a bit variable. The main problems are that sometimes the voices merge or are mistimed, cued, whatever. I’m not sure if this is a problem with 3rd party Skype recording apps (I have tried two) or with Skype itself. A quick Google seems to indicate that my troubles are far from unique.
If you are experiencing similar problems here is the simplest ghetto solution I can think up:
Next time you want to record your Skype conversation use an external recorder of some kind. With an iOS device try ClearRecord, otherwise use any wav capable digital recorder and simply record the conversation (the other person via the speaker + your voice).
Same with recording audio trailers from the computer- just sit still while your external recorder records audio from your speaker.
Pros: No weird echoes, no feedback, no EM noise and proper separation of audio sources.
Cons: Environmental background sound.