These are really two different questions: Wht is the effect of humans on the evolving global ecological system and what would be the effect if humans were to be exstnguished. The first answer is ... profound. As a dominant species we are an integral part of the global ecosystem. Our programs of deforestation, hunting, pollution, etc. have been a critical factor in its accomodating changes. The ecosystem at present is one that reflects our tenure on the land and, over the last century, our ill-use of it. The result is climate change, species extinction, etc.

 It is unlikely humans will disappear from the earth. It is very possible that the changes resulting from our industrial tenure will result in a catastrophic reduction in human population. This will be from economic collapse, climatic changes, new diseases, etc. So that would reduced our place in the world as a species and, depending on the nature of the catastrophic trigger, our continuing effect on the ecologies of the world. Anything more specific would be just speculation.

But it's also fairly clear from a series of studies that were we to cease to be, or cease to be as industrial beings, that the world would reclaim it's own. Buildings would crumble in the process that promotes fundal, bacterial, and plant habitation of our built materials. Air quality would change (after 9/11 we saw an example of this when jets were grounded and the air became clearer), water quality would change, etc.

My question is not really about the degree of our effect on the ecosystem of the planet, but about the nature of it. All things considered, is it a positive or a detrimental overall effect? That question can be addressed by assessing the most scientifically plausible effects of our hypothetical sudden removal.

The changes you cite... those are the obvious beginnings. I'm looking for models (probably computer generated) that can project into 100 - 1000 years after our hypothetical sudden disappearance. The studies you point to would be interesting to see, depending on how far into the future they project. Could you kindly point me to them? Thanks!