The MySQL "general query log" is very useful for situations where you're trying to figure out and improve or debug a large, complex app. The problem we often run into is that Hibernate logs, JBOSS logs, or other app-level logs miss queries or don't put constant data into queries, or the app itself has a bug in it that results in queries not being logged correctly or at all.
On the other hand, MySQL's "general query log" captures all queries sent to the server when the
system variable is set to 'ON'. A useful way to capture a particular application dialog is to run the app on a lightly-trafficked database instance, preferably an isolated test instance, enable the general log with
mysql> set global general_log = 'on';
quickly do your operation, and then disable the general log with
mysql> set global general_log = 'off';
After this, look at the log. It will have lines starting with a time, a connection ID, some sort of code indicating what happened, and the query text. Figure out which connection ID(s) are interesting, use "grep" on the log to get the lines belonging to the connection IDs of interest, and redirect this output into a SQL file. This can then be edited down to the actual queries (if you remember to put a semicolon at the end of every line), and you can make a simple script that can be run using mysql's shell-level tools.
These are very useful for debugging, benchmarking of the database accesses done by web or GUI-driven applications, or other SQL-based testing.