I believe Centos uses

/etc/sysconfig/iptables
/etc/sysconfig/iptables-config
and scripts in /usr/share/system-config-securitylevel/ for the GUI to set
open ports.

The file that matters is /etc/sysconfig/iptables
it generally looks like this (I grabbed this from a centos5.5 box):

# Firewall configuration written by system-config-securitylevel
# Manual customization of this file is not recommended.
*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
:RH-Firewall-1-INPUT - [0:0]
-A INPUT -j RH-Firewall-1-INPUT
-A FORWARD -j RH-Firewall-1-INPUT
-A RH-Firewall-1-INPUT -i lo -j ACCEPT
-A RH-Firewall-1-INPUT -p icmp --icmp-type any -j ACCEPT
-A RH-Firewall-1-INPUT -p 50 -j ACCEPT
-A RH-Firewall-1-INPUT -p 51 -j ACCEPT
-A RH-Firewall-1-INPUT -p udp --dport 5353 -d 224.0.0.251 -j ACCEPT
-A RH-Firewall-1-INPUT -p udp -m udp --dport 631 -j ACCEPT
-A RH-Firewall-1-INPUT -p tcp -m tcp --dport 631 -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state ESTABLISHED,RELATED -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 22 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m udp -p udp --dport 137 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m udp -p udp --dport 138 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 139 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 445 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 443 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 80 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 1158 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 1521 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 2100 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 5900 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 5901 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 5902 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 8080 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 9704 -j
ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m udp -p udp --dport 9704 -j
ACCEPT
-A RH-Firewall-1-INPUT -j REJECT --reject-with icmp-host-prohibited
COMMIT