This post may help others (and is a selfish post so I can check it again in a year when I get this next):
We were suffering server instability as follows:
- People couldn't login or use system
- No errors were showing in logs
- Both Tomcat and Aware Server were still running
We managed to narrow it down to a user upload, on a multi doc upload, causing the problem. It was a doc of reasonable size (5mb) but we had increased allowed packet size in MySQL my.conf to deal with it so we didn't initially think this could ne the problem. We then discovered errors in the MySQL log as follows:
ERROR: the age of the last checkpoint is 9445469, which exceeds the log group capacity 9433498.
Recommended solution here:
http://serverfault.com/questions/293406/mysql-innodb-error-the-age-of-the-last-checkpoint-is-x-which-exceeds-the-log