The assortment of chromosomes that the zygote recieves from the two gametes is primarily generated in three main ways.
The first is chromosomal crossovers, during prophase I in meiosis, when homologous chromosomes are paired together, there are points along the chromosomes that make contact with the other pair. This point of contact is deemed the chiasmata, and can allow the exchange of genetic information between chromosomes, giving a new combination of alleles on each chromosome
Good Diagram: http://www.emc.maricopa.edu/faculty/farabee/BIOBK/Crossover.gif
The second is Indepenadant Assortment which occurs in Metaphase I when the chromosomes are lined up along the equator of the cell. As there is a 50:50 chance of which way round a pair of homologous chromosomes will be on this equator, when the cell divides there will be a 2^n (n being haploid number of chromosomes) possible combinations of paternally dirived and maternally derived chromsomes in the daughter cell.
The final factor that causes variation is the random fusion between gametes, i.e. which gametes are involved in fertilisation, as genetically they will all be different.