There never was a check on them. It’s a fundamental flaw in the Constitution:
http://www.constitution.org/afp/brutus11.htm
I always figured impeachment could be a check. But getting enough representatives to take time from “legislating” and enough Senators to convict is probably impossible.
I'm not a lawyer, but is seems to me the executive branch has a nearly limitless check on the judiciary. It's called a pardon. I suspect all of the states governors have the same power in their jurisdictions as well.
As far as I know, the chief executive can overturn any conviction, any time, for whatever reason.
Perhaps this only applies to criminal cases, but the argument that the judicial branch does not have any checks from the executive always ignores the pardon.
Fixing that flaw requires amending the constitution. Something Perry is advocating by proposing term limits for Judges. Not Newt.