You do not need apply-log for the backup, but you need it for the restore. Depending if you perform differential or incremental backups, you will need to execute one apply-log for rolling forward the backup and application of the changes since the last full or incremental backup.
--apply-log --redo-only --incremental-dir
Whether you perform that after the backup or before the restore is entirely up to you and your backup policy. Some people prefer to have a ready-to-copy-back rolling-forward full backup, so they execute the --apply-log just after the backup. Others do the whole process just in case of the restore is needed. Both approaches have different properties in mean time to recovery, detection of faulty backups, space needed, time to perform the backup, etc.
Think on your recovery policy (not your backup strategy) and make the tool suit to it, not the other way round.
More info: http://www.percona.com/doc/percona-xtrabackup/innobackupex/incremental_backups_innobackupex.html