While I do not wish to start a debate why one needs to OPTIMIZE one's WordPress tables as often as one backs them up*, regular optimizing is crucial for tables with several variable-length rows that get many INSERTs and DELETEs, e.g.,
As it happens with the
wp-db-backup plugin, this is easily done by adding only one line to the source code.
$wpdb->get_results("OPTIMIZE TABLE ".implode(", ",$tables));
The line should be added just before the
foreach ($tables as $table) line in the
db_backup function. It's at line 897. Note that this affects only the scheduled backup process and not the one via the Admin screen --- that would require another line. :)
*It's debatable, but Yoast seems to agree with me (Tip #17/slide #37).