There are a lot of mods I dislike but there are a few exceptions. For example I think the red smoke mod on WOZ is a vast improvement over the original witch... although I'm not sure it is in the same category as its a replacement of an existing element and not an addition of a new element.
My TZ came from an operator and was completely stock other than LED's. Stock looks great and I think that game looks amazballs as is. I may add a couple functional mods such as the GLM mini playfield switch kit, but I don't think thats heresy.
I do not like the light strips above or below the playfield. My opinion is that if an area of the playfield is dark its that way because the designer intended it to be. Further its even worse if a game has a lights out mode and those light strips stay on... totally defies the whole point.