BOT is a mod to the IPCop GUI to allow you to write advanced firewall rules, so the name may be a bit deceptive since it's not just for outgoing traffic. You can write firewall rules for ingress (i.e. incoming) traffic as well as egress (i.e. outgoing), as specified by any number of criteria, even date & time.
If you want to block certain types of traffic from leaving the network, you'll have to do it on a port-by-port basis. Otherwise you can block the IP ranges of the servers these applications use.
As for Skype, it works fine for incoming and outgoing calls on my network with no port forwarding required. Since there are so many people behind this firewall who are completely independant of eachother, it's not a very wise idea to do PAT whenever somebody wants to host something, IMHO. If I was in your shoes, I would just make it a policy that if it doesn't work with the firewall, "too bad". :)