Quick and Cheap
The quickest method for query review is indeed the slow query log, combined with a tool called pt-query-digest
An example process is to first set
long_query_time=1. Set it to 0 for most accurate results, but it might affect IO depending on load of the system.
Let the slow query log run for a period of time, such as 1 week, to capture a significant number of query samples.
pt-query-digest against the slow log.
This tool is free to use.
To use a similar process, but have it behind a GUI to know when queries showed up or have been checked, you can set up Anemometer
An enterprise solution
The previous tools mentioned come without much cost, but only focus on queries.
A tool like VividCortex will provide you a great view of the performance of your system, and help you drill down into the queries in many different ways.
The method VividCortex uses to capture queries is lower impact than enabling the slow query log.