No they are not within the gene. Genes only produce proteins and RNA which are used as structural elements of the organisms or as chemical catalysts for the functioning of the organism. The promoter regions are outside the genes in the non-coding part of the DNA. Genes are identified largely by working back from a stop codon. They are also identified by chemical analysis of a protein and then matching the protein with the gene that made it. As to the functions of junk DNA the functions we already have scientific proof of are quite varied:
Some studies have found that noncoding DNA plays a vital role in the regulation of gene expression during development
Over 700 studies have demonstrated the role of non-coding DNA as enhancers for transcription of proximal genes.
Over 60 studies have demonstrated the role of non-coding DNA as silencers for suppression of transcription of proximal genes.
Some studies indicate that non-coding DNA regulate translation of proteins.
From: Junk DNA (See article for references and more specific examples).
Non coding DNA (also called introns because they occupy the space between the coding DNA or exons) have another very useful role - to enhance the variety of proteins produced by an organism in a very efficient way:
The problem of identifying introns was compounded by the discovery that alternative readings of the genetic code exist in which "introns" function as exons.30 Some DNA behave as exons when expressed by one pathway, but as introns when expressed by another pathway.31 Both pathways can operate simultaneously, resulting in greater protein product variety.32
Termination codons are also sometimes deliberately bypassed, allowing the coding of a part of an intron in order to produce a specialized protein.
From: The Function of Introns
This discovery answered the nagging question produced by the genome project: how could the human body produce 100,000 proteins (which had already been identified before the project began) with only 35,000 genes.
Typically when you refer to a gene you are talking about not just the protein coding regions, but also the elements upstream which regulate its expression. Also introns break-up the protein coding region and may themselves regulate transcription. The stop codon is not where it ends though either, you have regions further transcribed downstream which will contain information which regulates how stable the mRNA is and how efficiently it will be translated. None of this is new to anyone and it is generally not what we are talking about when we are talking about Junk DNA. There are vast stretches of DNA in the genome which are nowhere near a gene or ceratinly not close enough to have any effect on gene expression via the mechanisms we know of. Perhaps there are indirect effects....?