In the past decade, a number of bioinformatics tools have been developed to perform comparative genomics studies in plants and animals. However, most of the publicly available and user friendly tools lack common standards for the identification of robust orthologous relationships between genomes leading non-specialists to often over interpret the results of large scale comparative sequence analyses. Recently, we have established a number of improved parameters and tools to define significant relationships between genomes as a basis to develop paleogenomics studies in grasses. Here, we describe our approaches and propose the development of community-based standards that can be used in comparative genomic studies to (i) identify robust sets of orthologous gene pairs, (ii) derive complete sets of chromosome to chromosome relationships within and between genomes and (iii) model common paleo-ancestor genome structures. The rice and sorghum genome sequences are used to exemplify step-by-step a methodology that should allow users to perform accurate comparative genome analyses in their favourite species. Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits.