What happens to the goo?

I would imagine it remains dormant until someone tampers with it. Unsure really. But just like an Alien egg, the Ampules undergo a chemical reaction when it's surroundings are changed or affected in some way. So, who knows if it eventually leaches into the Planet's surface. Perhaps they can be triggered through radio waves, or some form of control the Engineers have developed.

Maybe it morphs lizards into T-Rex & we have another problem?

I can only assume that once activated the Goo only has a period of Half-Life before the substance becomes ineffective. It also appears that the Goo once it mutates a Organism can not further Mutate it. My theory was the Goo breaks down a Organism and then passes that Organisms DNA onto any Organism that it comes into contact with so that Organism mutates into a Hybrid. Thus if you had a Snake effected by Goo and broken down and the broken down substance then comes into contact with say a Cat you will have a Cat Mutated that takes on Snake and Cat DNA a Hybrid and if this Hybrid once its mutated comes into contact with the substance it has no further effect on the new Hybrid. I say this because if not well the movie leaves another plot hole, unless once the substance is released after a period of short time the Goo no longer has any effect. The above is based on the Goo being 2 things and thats its basic form like at the Start of the movie that breaks down a Organism into a new substance that contains and passes the victims DNA onto what ever it comes into contact. And that the Urns do not contain the above but the resulting broken down Material, i.e the Urns contain what ever happens to something once it has ingested and been broken down by the Sacrificial Black Goo. Again the Weyland Viral File does not support that theory and instead well creates a more complex process that has many potential holes than it did in the first place.

I would imagine it stays dormant until tampered with once more. The again the atmosphere changes made the cannisters burst and the goo active so possibly it will spread about slowly.

[i]"Does it effect [sic] the planet/atmosphere?"[/i] Nobody knows. [i]"Does it go back in the urns by itself?"[/i] I'd find that a little implausible. Since it's contained in sealed glass vials, it would have to get back in. [i]"Or just stays in puddles?"[/i] That's my guess. It could remain deadly in perpetuity. In which case, there would need to be something like a white goo that could be dumped on a planet to neutralise it. Or, as Big Dave suggests, it's been designed to self-destruct after a certain amount of time has elapsed. I quite like the idea of a white goo, myself. Holy canisters splashing down into deadly blackness destroying the destroyer. Sounds like fun.

sounds like a crazy monochrome paintball war

Yup. Anything as alien as this is going to seem crazy to a human. It could get even weirder, like Quantum Mechanics: "It's not only stranger than you imagine, it's stranger than you [i]can[/i] imagine."