This is for humans:
See wiki for some rough estimation: 20-40%
"20-40% of the genome is gene regulatory sequence"
Here the estimation is different:
"The idea, Birney said in 2012, is that the 8% is nearly all regulatory sequences, DNA that governs the behavior of the 1 percent of DNA that codes for proteins. He noted that, until the ENCODE project, scientists thought regulatory sequences would take up about the same amount of space as protein-coding sequences. It was a big surprise to learn that the DNA that regulates genes was eight times bigger." "The new paper largely confirms what Birney said in 2012. One of the Oxford scientists, Gerton Lunter, told me in an email that they can’t give an exact breakdown of what functional categories constitute the 8.2 percent, but they have concluded that basically all protein-coding genes are there. All, or nearly all, regulatory material forms a large contribution, too, he said."
On the other hand:
"Significantly, more than 4 million regions that appeared to be regulatory regions, or "switches," were identified. These switches are important because they can be used in different combinations to control which genes are turned on and off, as well as when, where and how much they are expressed. Effectively, this provides precise instructions for determining the characteristics and functions of different cell types in the body. Changes in these regulatory switches, especially those regulating critical biological processes, can thus influence the development of disease. The astounding amount of gene-regulatory activity uncovered in the human genome is striking, as more of the genome encodes regulatory instructions than protein, and prompts an assortment of complex questions on how the genome is involved in health and disease."
This is for bacteria:
Just search for "regulation" in this table.
General theory for eukariotic organisms: