The command line is important too.

I've worked with databases which are difficult (or impossible) to work with in PHP as they're simply too big. Exporting a giant database with PHP, can often timeout long before the database is exported.

Using the command line avoids those problems. What might take an hour to export via PHP, can be done in 30 seconds or so via the command line. There is a huge performance advantage, and I've never had anything time out when done via the command line. It'll just keep on chugging until the task is complete.