Currently Moodle uses tables to generate the page layout. While they do appear to work, tables are not intended for page layout, and divs offer more flexibility and customization with the evolving web standards.
The proposed solution is to replace the layout table with floating divs.
A container div is required, with margins on both sides set to the block width (these margins can be optional based on whether there are blocks on the page or not). The left column would be stored as a floating div, followed by the right column, followed by the actual content for the centre.
This system has already been tested with 1.9 on our production site: http://www.thomashaney.ca/
The main issues are that it would require a rewrite of many themes. With that in mind, it would be best to mark it for 2.0 rather than 1.9.x so as to not break existing themes.
I can provide a patch for the standard theme .css files and the index.php as an example.