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There are a number of reasons why you might want to use other port numbers than those provided by default. Most common startup problems are in fact associated with port conflicts. You can use monitoring utilities like Active Ports that will quickly tell you what application or process is using what port so you can customize Geronimo's ports accordingly. On Unix-like platforms, you can always use something like netstat -nao | grep -i list to get the ports in use along with what application is holding that port. Alternatively, you can use netstat -nab on a Windows platform.
Note that ActiveMQPort setting in the config-substitution.properties file does not work. If you want to change the port number for ActiveMQ server, update the value of portOffset in etc/blueprint-activemq-placeholder.cfg file.