In my recent internet queries to find the ultimate DB software, I stumbled upon a gem of a program by FabForce.net. Its called DBDesigner. This program is quite amazing for building tables and databases for visual programmers. I usually do a pensil or pen diagram of how i want my table layed out, then rough it in to excel or something. After that i write the PHP code to build it or go into PHPMyAdmin and do it manually. This program automates this whole process for you and includes linking tables, a query search within your tables, and you can download and sync your tables all within it.
Check it out when you get a chance! http://www.fabforce.net/dbdesigner4/
It may even help old schoolers like me get into shape with making cleaner tables.