On a purely mundane level, i'd highly recommend that you research the particular stone you're working with BEFORE using any kind of solvents or methods--some stones are easily damaged. Mother of pearl and some kinds of shell, for instance, can be permanently damaged by certain substances (i forget which ones, currently, but usually harsh solvents are suspect w/ organic minerals). For some stones, particularly those whose chemical compositions do actually contain water, it can be helpful to soak the stone every so often--it sounds weird, but it works to keep the stone shiny and full-colored. Chrysoprase is like that:
http://www.rings-things.com/gemstone/c.htm. Some stones, like aquamarine, may become paler in sunlight, which can't really be fixed as far as i've heard. Other stones might be heat-sensitive. Those which fracture easily, like flourite, are particularly susceptible to sudden marked temperature changes, while amber actually melts in certain temps. Learning the chemical compositions of certain stones and figuring out which ones are most closely related to each other may help as well--for instance, if you know that heat and light can change the color of an amethyst, you might want to be careful with your citrine as well, just as a precaution.