MySQL Workbench
“MySQL Workbench is a cross-platform, visual database design tool developed by MySQL. It is the highly anticipated successor application of the DBDesigner4 project. MySQL Workbench will be available as a native GUI tool on Window, Linux and OS X.” Currently beta but check out the screenshots.

phpMyAdmin
“phpMyAdmin is a tool written in PHP intended to handle the administration of MySQL over the Web. Currently it can create and drop databases, create/drop/alter tables, delete/edit/add fields, execute any SQL statement, manage keys on fields.” Web-based, very mature and stable product.

MySQL Query Browser
“MySQL Query Browser is the easiest visual tool for creating, executing, and optimizing SQL queries for your MySQL Database Server. The MySQL Query Browser gives you a complete set of drag-and-drop tools to visually build, analyze and manage your queries.” Includes simple but solid tools for building and managing databases and tables.

Ferret
“GNU Ferret (formerly known as GerWin) is the Free Entity Relationship and Reverse Engineering Tool.” Development seems to have stopped which is too bad because it has potential.

And here are links to some more database design applications (some commercial) at del.icio.us.