You can add system properties when running Tomcat (mvn tomcat6:run). The syntax has the following format:
<project>
...
<build>
...
<plugins>
...
<plugin>
<groupId>org.apache.tomcat.maven</groupId>
<artifactId>tomcat6-maven-plugin</artifactId>
<version>2.3-SNAPSHOT</version>
<configuration>
<systemProperties>
<example.value.1>alpha</example.value.1>
<example.value.2>beta</example.value.2>
</systemProperties>
</configuration>
</plugin>
...
</plugins>
...
</build>
...
</project>