SNMP + external server
http://forum.mikrotik.com/t/simple-queue-save-statistic/8293/1
Netflow + external server
http://forum.mikrotik.com/t/how-to-get-bandwidth-usage-details/46366/1
Save stats on router in comment field of queue / interface, would need to be scripted
http://forum.mikrotik.com/t/how-to-get-bandwidth-usage-details/46366/1