You can set tomcat environment variables by setting the JAVA_OPTS variable in /usr/share/tomcat5/conf/tomcat5.conf.
I needed to do this when using JDBC over SSL to connect to MySQL. I had to tell Java the location of my keystores:
JAVA_OPTS="-Djavax.net.ssl.keyStore=/tmp/certs/keystore -Djavax.net.ssl.keyStorePassword=changeit \ -Djavax.net.ssl.trustStore=/tmp/certs/truststore -Djavax.net.ssl.trustStorePassword=changeit"