FQDN is short for Fully Qualified Domain Name. Refers to an internet DNS name, complete with top level domain (TLD), resolvable from any network anywhere without special help.
For example, ph34r is a server name, but ph34r.tehinterweb.net is an FQDN. If you happen to be a member of the tehinterweb.net internet domain, you can simply type ping ph34r and get DNS resolution, but if you're, say, a member of coxcable.net, you would need to use the FQDN and refer to it specifically as ph34r.tehinterweb.net.
note: this is not a FreeBSD-specific term.