How to handle huge sales_flat_quote tables - remove abandoned cart refuse

DELETE FROM sales_flat_quote WHERE updated_at < DATE_SUB(Now(),INTERVAL 60 DAY)

sales_flat_quote and it's related tables use foreign key relations to delete on cascade so deletions in the primary table deletes all related entries automatically in the other tables.

Once you get it down in size, you can easily modify the observer (obligatory make a module here) that's supposed to clean out expired quotes to include all quotes as is done in the first link with customized retention for abandoned cart recovery and retention of logged in customer quotes for a reasonable period so your customers don't get mad when their cart empties unexpectedly: Are unconverted quote records ever removed in Magento?

or use Fabrizio Branca's AOE Quote Cleaner

sales_flat_quote* tables contain shopping cart contents. This is known as a quote and is held until the customer decides to finish placing the order. For finished quotes that have been converted to Sales-Order, Magento automatically clears them with a cron job. The logic was never extended to include open quotes.