See this blog post which explains it all.
The trick in FreePBX is to create a CUSTOM extension and in the “Dial” setting use this:
That will get you the Skype “echo test” (or their version thereof). To call a different Skype user, repeat but replace echo123 with that user’s Skype ID.
Calls are limited to five minutes (apparently there’s a paid service if you need to make longer calls) but if you exceed that you could always call back (or fire up a real Skype client). But this could be handy for quick calls where you don’t want to power up a computer and access a Skype client just for a quick one or two minute call.
EDIT: Or now you can “roll your own” SIP to Skype gateway - NO time limit, and you can receive incoming calls!
Why Wait? Build Your Own Skype Gateway to Asterisk