We describe some unexpected features of pseudogenes in diverse organisms that are inconsistent with the traditional view that considers pseudogenes as nonfunctional sequences of genomic DNA (“junk” DNA) not subject to natural selection. Pseudogenes are often evolutionarily conserved and transcriptionally active. Moreover, there is evidence indicating that some pseudogenes engage in regulation of gene expression and generation of genetic diversity. Pseudogene patterns of nucleotide variability evince that not all pseudogene mutations are selectively neutral and, thus, do not all have equal probability of becoming fixed in the population. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection, if the source gene remains functional. Therefore, alleles of the pseudogene will accumulate mutations, including disabling mutations, over time. But a mutant allele that incorporates a new function may be favored by natural selection and will have enhanced probability of becoming fixed in the population. Thus, some pseudogenes that have lost the original function may have acquired new ones. A review of the evidence leads to the conclusion that pseudogenes are important components of genomes, representing a repertoire of sequences available for functional evolution and subject to non-neutral evolutionary changes. Pseudogenes might be considered as potogenes (following the terminology of J. Brosius and S.J. Gould, 1992), i.e., DNA sequences with a potentiality for becoming new genes (Balakirev and Ayala, 2003). Furthermore, we conjecture that some pseudogenes along with their parental sequences may constitute sets of indivisible functionally interacting entities (intergenic complexes or “intergenes”), in which all the component elements are required in order to fulfill a collective functional role.