Skype is able to use a SOCKS5 proxy and therefore can be used with Your Freedom (you need to activate the SOCKS5 port in the YF client on port 1080, but this this default configuration). But there is a very nasty problem with that: even if you configure one in Skype, it will only be used as a backup means of connection, by default all connections will still be direct. However, there is a means to force Skype to use a proxy, and it is described in the IT Administrators Guide. In short, you need to tweak the Windows registry (for other OS, you are on your own... sorry).
You need to add these keys to the registry:
To return to the default behavior, change "ProxySetting" to an empty string and set the two dwords to 0 -- or simply delete the whole key [HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Skype].
To make matters simple for you, we have created two .reg files that you can save to your Desktop and run as needed. One will make Skype go through Your Freedom, the other will restore the default behavior. Please be sure that you exit Skype first (not only close the window... the icon in the task bar needs to disappear; right-click on it to exit Skype) and restart Skype after you have imported the registry values.
After making the alterations to the registry, we strongly recommend to make a test call and verify that it is going through Your Freedom (it should not work unless the YF connection is up!).
Please note that whatever you configure in Skype's options dialog will only be used in case a direct connection is not possible. If you rely on hiding your activity behind YF, this is not what you want to do. Use the registry tweak! Everything below only applies if you do not want to use the registry change and stealthiness is not an issue for you.
(Of course, you need to use the same port you have used in the Skype configuration, and it must be a port assigned to you, check the Profile tab in the YF client when connected.)
If you are not a TotalFreedom user, configuring a server port forward is useless and it does not matter what you configure in Skype. Skype will work nevertheless (but you might have more delay).
Now save your settings and restart Skype. Be sure you really quit Skype, just closing the window is not enough. Then start Skype again and log in or create an account.
A note on choosing Your Freedom servers: to avoid unnecessary delay you should try to choose a Your Freedom server that is close to you. We have servers in Europe and in the US, choose one that is as close as possible. Of course, any will do if none is close to you but you may experience delay.