One of my website’s database grew to 5.5Gb in size. When it’s that big phpMyAdmin and standard control panel backup scripts just don’t work. Fortunately there is a great solution: MysqlDumper.de (english translation). It’s PHP/AJAX application that backs up and restores your databases part by part. It’s really straightforward to use.
It took it 10+ hours to export by 5.5Gb database as 700Mb of GZipped SQL scripts but it got the job done 100%. Another nice touch about it is that it allows you to break down your backups into parts so you can start restoring the database at the new location the moment first part is ready. This can be quite useful since when you are restoring database this big reconstructing indexes can take a very long time.