I don't use Skype so haven't tested the below, but you could give it a try.
According to the unofficial skype blog at http://www.skaip.org...rs-for-the-new-skype
you can start a Skype call from the command line with a parameter like this
So I suspect that an alias looking something like this will work
Alias: skype call
regex: ^skype (.*)$
results: C:\folder\skype.exe --_="skype:$$1?call"
But with the correct path to skype.exe or whatever the executable is named. Also maybe the " characters may need to be escaped.
Once that is tweaked to work you then input this into FARR and press enter to start the call