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As per wikipedia definition, gene density is defined as:

"In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in terms of a million base pairs, or megabase (Mb). The human genome has a gene density of 12-15 genes/Mb, while the genome of the C. elegans roundworm is estimated to have 200."

But I would like to know in what circumstances one would consider gene density as an important parameter? To be specific in what kind of experiments the model organism's gene density plays key role?

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    $\begingroup$ I don't know about experiments, but it might be useful in estimating size of exons & predicting length of mRNA. $\endgroup$
    – another 'Homo sapien'
    Commented May 23, 2016 at 6:38
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    $\begingroup$ Of the top of my head two fields that could make use of gene density arw Bioinformatics and evolutionary studies. Gene density says something about complexity of organism, information storage, etc $\endgroup$
    – SciEnt
    Commented May 23, 2016 at 16:55

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This is an open-ended question and will be impossible to correctly answer. I am voting "to close as too broad". Note also that the question in the title is not the same as the question in the post.

But I still wanted to give you some information that may help you. Here are just a few examples for which knowing gene density matters.

Background selection is the process by which purifying selection reduces heterozygosity at nearby loci. Knowing the density (and positions) of genes (and other sequences potentially under selection such as regulatory sequences) is essential to understand the variation of background selection throughout the genome. Being able to design maps of variation of background selection throughout the genome is essential to improve our ability to detect local adaptation and positive selection as background selection leaves similar genetic signature.

The evolution of the genome size is in itself of interest to evolutionary biologists. Species having large genomes ave large genomes mainly due to repetitive neutral sequences. As such the question of gene density is essential to understand the evolution of genome size.

The gene density varies throughout the genome (with a variance greater than the mean, that is it does not follow a Poisson distribution). Understanding the evolution of gene density at different regions is of interest to many. Note that interaction effects among genes also depend on their physical distance.

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"Note that interaction effects among genes also depend on their physical distance." I think that's more of a pragmatic assumption, because we tend to associate regulatory features with their closest downstream TSS, though it's certainly not a hard and fast rule. e.g., in certain organisms like budding yeast, its known that the most transcription factor binding sites are downstream of gene bodies. even in humans, the association is not entirely clear as there are both cis and trans effects especially notable with things like super enhancers and things of that nature. Or consider the following, http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004461

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