Great question Jean, from the few I have done so far I find

1) ensure the call is half one and then half the other.  It ensures that everything is fair

2) prepare something you want to talk about, for instance talk about a newspaper article or a section of a book you can both read

3) when you spot a clear problem the other person is having and you know a solution, dig it out and give it as a gift.

4) take notes

5) smile, even if you are both struggling, keep it fun and when confusion grows, stop and start again until the meaning is clear.

6) skype stutters, just be patient

I'm really looking forward to seeing other people's views on this

It totally depends on the comfort level of your partner. Usually I offer the option of switching every 30 minutes to each other's maternal language or I speak in English and they respond in Spanish. Very few take the latter option.Personally I think it is better to concentrate on one language at a time. 

I like to come prepared with questions I need clarification. I also ask if they need specific help in any area.

And I write down notes of course so I remember the new words I learned.

Buena suerte!

Good points Bill ! One thing I have learned also from experience is to keep track of each other's speaking time. I have had partners who want to continue speaking in the language they are learning and don't seem to want to switch or are too gracious or too shy that they want us to be speaking Spanish ( the language I am learning) most of the time and I usually persuade them to start talking in English so they can practice.  

I find the challenge in these intercambios is the consistency. Schedules  and time differences vary.