I was doing some VoIP testing this morning with a friend and he was surprised by how bad my voice sounded. His was perfectly clear. I finally realized that I had a BitTorrent transfer going on another machine. Whoops!
I've been meaning to add traffic shaping for a long time and that was the last straw. I found a script that seemed simple enough but after running it I found that my SPA-2000 no longer worked.
Through trial and (much) error, I discovered the culprit was a command that reduced the MTU to 576. Disabling that eliminated the problem.
I did some more testing while doing transfers. Much better.