Use stored procedures for all your updating/inserting/deleting The procedure should take all the arguments it needs to perform the given task plus one argument that will contain the comment. Then just update/insert/delete and make a record (with the comment) in the log table.
ps: can't see how you would be able to use some tool if you need to insert comments (same problem than triggers).
I definitely prefer doing this in application code rather than in the DB. An ORM is wonderful at handling this kind of thing as it gives an easy way of tracking and intercepting changes.
If you have a sensible abstraction over your database access then it should be pretty simple to intercept any database calls in your PHP code and do the logging there. Of course if you are building up SQL manually and then calling the database directly there is no central place for you to log changes.
phpmyadmin supports database replication and tracking changes since the latest version