backup huge databases

1) replication.
Production database - Master. Replication to slave base in another server. Stop slave base and make backup from.
2) xstrabackup. Free software from Percona. Nice for InnoDB!
http://www.percona.com/software/percona-xtrabackup
http://form.percona.com/rs/percona/images/Percona_XtraBackup_20_Operations_Manual.pdf
http://www.youtube.com/watch?v=Hf31NJvjr_E

to read:
http://habrahabr.ru/post/63394/
http://habrahabr.ru/post/137380/