The question gruntpain is asking is whether the court can actually make their decisions apply to the entire military, or only the parts of the military within the 9th circuit.
I think so. If a company has offices in both Arizona and New Mexico (9th and 10th circuits), and they are involved in a lawsuit that forces them to do something as a whole, their New Mexico branch is not immune from the decision, as they are a single entity. The defendant in this case is the United States, and is treated as a single entity. However, their decision is not binding precedent to the other districts, so while there may be an injunction against the military enforcing don't ask don't tell globally, the law is still technically constitutional in the other districts. These inconsistencies between circuits are why the Supreme Court takes a lot of the cases it does, so I expect the matter to go up the ladder shortly. Plus, I don't think this ruling is going to make the gays come out en masse until the Supreme Court rules, so I doubt it will change much practically except that people who accidentally get outed somehow will get to stay in for now and won't be sure of their long term status until after the Supreme Court hears it, as either the Appeals or the Supreme Court could reverse.