Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).
Nothing in that implies that a piece of DNA has any function useful to the organism.
Another view.
The main ENCODE paper says:
Nothing in that implies that a piece of DNA has any function useful to the organism.
More controversy.