Preferred Method of debugging a wordpress SQL calls?

Turn on define( 'WP_DEBUG', true ); and define( 'SAVEQUERIES', true ); .

I prefer the format of the debug bar, http://wordpress.org/extend/plugins/debug-bar/ , which can be combined with the console, http://wordpress.org/extend/plugins/debug-bar-console/ .

This script is great for profiling, Best Collection of Code for your functions.php file

There are some other plugins that might help, like Debug Queries, but you probably going to have to use a debugger like xdebug to get more fine grained details.