A little late to this, but I have the answer for blocking File Transfers in Skype. Unfortunately it' s a registry key that needs to be added, and not a FortiGate setting.
Here' s the administrator' s guide, it works with the most recent 6.1 release as well (Appendix 1 has the configurable policies). So in example, to block file transfers, you will need to add this registry key:
HKEY_CURRENT_USER\Software\Policies\Skype\Phone, DisableFileTransfer, REG_DWORD = 1
You will likely have to add the Skype\Phone hive, so it' s best to do this via GPO or a .reg file.
...And I can' t find any mention on doing a similar function on Macs, sorry.
Security Analyst, Network Engineer, Part-Time Everything Else