Sometimes good is not enough. As we move on to design larger and more complex databases the tools we use also need to change. Managing InnoDB relations in large databases becomes a pain even with tools as good as phpmyadmin. Enter the visual database design system. The problem now is usually cost related. Most of these tools are expensive, and usually not targeted towards the databases that are common in the PHP world.
I recently discovered DBDesigner 4 from fabFORCE, a OSS tool that runs on both Windows and Linux besides offering support for MySQL, Oracle and plain ODBC. I have tried a couple of OSS tools in this area, and so far this is the best one I have come across, but don't take my word for it, go to http://www.fabforce.net and try it out.
There are of cause bugs, missing features etc, but the developers are quite responsive, and new versions are released frequently. Worth to mention is that the tool also supports InnoDB in MySQL including foregin key restrictions etc.