???
Squid wouldn't affect the working of these programs and can't since Squid is a http proxy, not a proxy for other protocols such as ftp, pop3 and smtp. If the software worked before Squid and you haven't touched the configuration of these programs since, then there's no reason for them not to work now. If you have configured these programs to somehow use squid then you need to reset the configuration to what you had before. As far as I'm aware (and I have played with this at home a fair bit) the only thing that would stop your programs from working would be firewall related.
In short words, what you want is not possible with Squid. Squid can only cache and handle http requests.
ICQ (for example: Netscape 7/ Trillian, ...) works with Squid and FTP works with Squid. (for example: Netscape)
I don't use those other program, so I cannot tell that.
rgrds,
Bart
