Intermittent engine vibration

It is working okay, but I notice that every so often when I am traveling at a steady speed the engine feels like it is 'lugging down'. At highway speeds even on cruise control when this happens there is a vibration (noticeable by everything in the rear view mirror shaking) and you can hear the engine sound change. Initially I thought it might be an out of balance wheel but I had to replace one of the run flat tires (do not get me started on that) and I rotated the tires on that side. It made no difference in the intermittent vibration I am experiencing. Note: this happens at lower speeds, too. It is just not as noticeable. I bought the car used with 108,000 miles; it now has 129,000 miles. I have changed oil a few times, but no other maintenance to speak of. In the back of my head I am hearing 'change the plugs and the air filter', and recently that voice asked 'what about the PVC valve?' This problem also occurs for a short while when I pull my foot off of the gas. That same voice is telling me it could be a 'breathing ' issue. What are your thoughts?