You might want to take a look at MySQL Workbench. I have found it the best program I have come across for generating E-R diagrams of your databases and creating MySQL table schemas in that you can then export as SQL structures.
As just a query designer, however, it may not be suitable. But for anyone who regularly has to design and document MySQL databases it is well worth a look. http://dev.mysql.com/downloads/gui-tools/5.0.html There is also a version in the Ubuntu repositories. Guy.
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