It's all about the ACKs

I've recently set up VOIP (via engin) and did not want my other net activities to interfere. I had my download client throttled to 5kps and I was running wondershaper but it didn't seem to make a difference. It finally dawned on me that it was my ACK packets that were flooding my upload link. Once I added some iptables entries to mark the packets from my download software, and gave them the lowest priority, all was good.