The simple solution is to prioritize by DSCP (TOS) value. There is a script on this forum that does it automatically.
See this topic: http://forum.mikrotik.com/t/fasttrack-friendly-qos-script/102401/1
This works OK for applications like VoIP because the writers of those applications usually set the right DSCP value in their packets.
When you have other applications that do not do that correctly, it is the fault of those applications, not of the mechanism.
However, when you merely setup a queue tree as done in the referenced topic, and you make sure your max speed is slightly below the real upload speed of your connection, you already improve matters a lot.