I can see from Wikipedia that there are possibly thousands of harmful mutations that have been cataloged and linked to disease. There are also unnumbered neutral mutations. But, does anyone know how many "beneficial" mutations have been cataloged in scientific literature?
That would be hard to say because really beneficial mutations become well distributed through the genome. Basically the differences between us and chimpanzees are a catalog of all the beneficial (or completely neutral) mutations since the ~4.7 M years since we diverged from each other.
Separating them from changes which have no special effect would be difficult too, but more to the spirit of your question, its difficult to explain what many mutations do, unless they cause significant changes in something we can observe in the individual (like height, weight, big nasty claws, etc).
For some more specific examples you can look at Online Mendelian Inheritance in Man. Some mutations which are useful sometimes might be related to skin color for instance (really helps when there is a lot of sun about) or lactose tolerance (a variation which is popular amongst europeans who have been drinking dairy milk for thousands of years).
Just continue scrolling down wikipedia: there are also listed two examples of beneficial mutations: the one conferring HIV resistance, and the one conferring malaria resistance.
Note that 'beneficial' is relative. The mutation associated to malaria resistance is actually causing sickle cell disease.
Others have posted that the term beneficial in genetics is contextual - single mutations may be harmless, unless another mutation is co-inherited; this is called epistasis (where more than a single mutation/genotype/allele is required for the phenotype).
I have not studied the list comprehensively, but there is a 'catalog' of all robust genome-wide association study results here. Depending on your outlook, all mutations associated with a disease are therefore also 'beneficial' if you have the protective allele and not the risk allele. Using this logic there have been many SNPs identified that are protective, rather than beneficial per se, and these are listed in the GWAS-catalog I linked to. As of 05/11/12, the catalog includes 1258 publications and 6400 SNPs.