The original decision is here (in German). It deals mainly with the question if the plaintiffs had enough opportunity to explain their point of view before the decision in question. That they did not have that opportunity was one reason the lower court said the decision was unlawful.
The Federal Court affirmed that opinion of the lower court.
What does that mean?
It does not mean that the shutdown of the nuclear plant in question (Biblis) is illegal even now. In the meantime the German legislator has decided with a large majority that this plant should be shut down from 8 August 2011 on.
Therefore, RWE (the plaintiff) may be entitled to some form of compensation. But they will never again be able to actually produce electricity with that plant.
Even if you are opposed to nuclear energy, I think it makes sense that someone running a nuclear reactor like the plaintiff RWE in this case gets the normal procedural protections of administrative law (e.g. the right to voice their point of view before a decision). And I think it is a good thing that German companies don’t put up with illegal behavior by regulators. Guarantees of fair procedure in administrative law are only worth as much as the readiness of such companies to fight for their rights.