Sorry, AirDroid now doesn't support this. Add tel://number
will lead you to skype when you click it.
You can also add a contact shortcut which allows you to call that contact.
Well that's the meaning of a feature request
In the browser I can set up which external programs are to handle some protocols.
Just like mailto: can be sent to different mail programs, tel: can be sent to skype, or my pc-desktop voip phone program, it can be sent to the airdroid desktop application.
I have actually tried setting AirDroid.exe, AirCmd.exe, Helper.exe and Launcher,exe as handlers for tel:url, but naturally, they don't know what to do with the number. (Luckily most programs are not more clever than their programmers yet :-) )
Remember, I'm not talking about airdroid running in a browser, I'm talking about the desktop app.