Since I redid my room and have new equipment, everything except xbox is now HDMI. I even saved the mess of 6 analogs from my Oppo to play SACD through HDMI. Only concern is my VTF2 woofer gets a bad sounding pop, say when I turn on my TV even though I am listening to the Oppo, or when I go into the setup menu of my SR8002. I countered by simply lowering the volume before turning on something (hence I don't hear the pop then), but is there any reason for concern or is this normal? Hopefully by keeping the volume low this "spike" or whatever it is won't adversely affect any of my equipment. Is this due to HDMI cables?

The receiver should be smart enough to mute the output when an HDMI negotiation occurs. It seems yours isn't doing so. When the state of the HDMI connections change the full HDMI chain has to renegotiate with each other.

For instance, when I'm listening to a DVD-Audio disc on my Pioneer DVD player, and I turn on or off my TV, the audio mutes while the receiver goes from being a repeater to an end point, the DVD player goes from outputting 1080i, to 480p. That takes a couple seconds, but then audio resumes without an pop.

I'd say it's a design flaw from the 8002 being an early implementation of HDMI, where not all the quirks had been discovered yet.