If you are using a Macintosh machine, there are a couple great options.

My first choice is 'Call Recorder', from Ecamm network. Not only does it do an incredible job of making it easy to record both sides of a skype call, but it can also record the video, if you are doing a video chat.

http://ecamm.com/mac/callrecorder/

Audio Hijack is also a good choice. More expensive, but it can do Skype, plus so much more. It's overkill if you just want to record a Skype call.

http://www.rogueamoeba.com/audiohijackpro/

Call recorder is the cheapest and simplest way to do it. No confusing setup, just install it and press record. When you are done, you will have a perfect dual sided Skype call. You can even extract each side of the conversation with a little more work.
Source(s):
http://www.rogueamoeba.com/audiohijackpro/

http://ecamm.com/mac/callrecorder/

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