I would *definitely* focus on your SQL queries:
1. Use Windows Task Manager (or better, Windows Performance Monitor) to identify which process is consuming resources, and specifically which resources.
<= IT SOUNDS LIKE YOU'VE ALREADY DONE THIS:
THE PROCESS IS "MYSQL", AND THE RESOURCE IS %CPU
BUT DOUBLE-CHECK: YOU MIGHT BE SURPRISED...
2. Try to identify specifically which query is causing you problems. You might already know the query, you might have to put "printf's" (excuse me - "System.out.println's" ;-)) in your Java program.
3. Run the query manually, directly from the "mysql" command monitor.
Use "EXPLAIN".
Perhaps your tables need some extra indexes; perhaps you might consider denormalizing them; perhaps you can just make a simpler (less expensive) SQL query.
Here's a good link for mySQL performance tuning:
http://dev.mysql.com/books/hpmysql-excerpts/ch06.html 'Hope that helps .. PSM