I have found that many of the java components (.jar) files found in the Tomcat/lib folder are outdated. 20+ components.
One example, upgrading to MySQL to 5.6 AwareIM still communicates with it through buggy version of Connector/J JDBC driver which is a few years old.

Anyway, I thought I would share the list of the components I have replaced. So far so good.
Instead of changing the AwareIM/bin/awareim.conf, I've renamed the latest files and simply replaced the old ones.

AS OF 22 MAR 2014

Apache Tomcat 6.0.39

activemq-all-5.8.0.jar to activemq-all-5.9.0.jar
mysql-connector-java-3.1.12-bin.jar - mysql-connector-java-5.1.30-bin.jar
axis-1.4.jar
Apache Commons (7 files)
- Beanutils
- Codec
- Dicovery
- Fileupload
- Lang3
- Logging
- Validator
  derby.jar
  ical4j
  iText-2.1.7.js2.jar
  jcommon-1.0.22.jar
  jfreechart-1.0.17.jar
  log4j-1.2.17.jar
  saaj-api-1.3.5.jar
  scribe-1.3.3.jar
  wsdl4j.jar
  xerces-2.4.0.jar
  Don't forget the latest tools.jar if you update the JAVA JDK.

Always keep backup of original files.
Replacing these files showed no server/tomcat startup errors in the log.

Cheers