This only affects research organizations and companies that use federal funding to perform embryonic stem cell research.
Anyone can perform any kind of stem cell research with private funding*.
There are some ethical problems many (not most) people in the US have with this type of research, and they've voted in politicians that every year vote to pass the amendment in congress that prevents federal funding from going to research that destroys embryos.
The federal judge has simply affirmed that congress, who has power over the budget, has control in this situation, and that the executive branch can write all the executive orders it wants, but it won't affect how federal funds are spent for this type of program.
This is simply a big paper-rock-scissors war between the three branches (executive, legislative, and judicial) and at the moment the judicial branch is supporting the orders of the legislative branch (congress) in defiance of the executive branch (president), primarily because it concerns federal funding, and this type of funding is clearly under the control of the legislative branch. It is their responsibility.
This is one of the areas the President is free to pander to the masses about. He can claim that he'll take the bull by the horns and get something done, and he'll take the credit when things go well, and blame someone else when things don't go well, and no matter what happens it will only reflect positively on him.
If people want federal funding for programs which destroy fertilized human eggs, they need to bother congress, who holds the purse strings, not the president.
-Adam
* Yes, there is a tangled web of financial issues that make it difficult for research institutions to work outside federal law even if they aren't accepting federal funding, but if they want to do so and they have the private funds they can make it happen.