I have gotten IBMJSSE to to work with Sun's JDK 1.4.2 and TOMCAT 4.1. This configuration also supports IBM Emerging Technology Toolkit. The entries in java.security are as follows
security.provider.1=sun.security.provider.Sun
security.provider.3=com.ibm.jsse.JSSEProvider
security.provider.4=com.ibm.crypto.provider.IBMJCE
security.provider.5=com.sun.rsajca.Provider
security.provider.6=com.ibm.security.cert.IBMCertPath
security.provider.7=com.ibm.security.jgss.IBMJGSSProvider
Further on down set
ssl.KeyManagerFactory.algorithm=IbmX509
ssl.TrustManagerFactory.algorithm=IbmX509
Hope this helps you out.