What organisms besides fruit flies have homeobox genes?
All animals, plants and fungi that we have the genome of!
Homeobox genes are very fascinating, because they are found in almost all organisms where we have mapped the genome (= all the DNA of an organism) of. This goes for animals , plants and even (unicellular) fungi .
These homeobox genes appear to be so essential in the early development of multicellular organisms that they have been highly conserved throughout evolution. See also this question for more information of the evolution of these genes.
I am not aware of any examples of animals, plants and fungi that have no homeobox (or homeobox-related) genes at all. Bacteria (single celled organisms) have genes that seem related to homeobox genes, but it is unsure to what extent prokaryotes need / use these genes.