Here are a few suggestions

This is a nice handy guide, but you should also look up stones individually to see the best way to cleanse them too. Some stones like Amethyst and Aquamarine are sensitive to sunlight and can lose their color and other stones like Calcite and Selenite can dissolve or become damaged in water. I usually use moonlight or incense.

This is from Cunningham's Stones and crystals encyclopedia (excellent book on the subject always useful for me) This is a simple process which removes any past influences from
the stone, readying it for our uses. It is advisable to do this for each
stone. The only exceptions are those which you yourself have collected
unless you found them near a military institution, a highway or
polluted ground.
There are a number of methods of stone purification. The simplest is to place the stones in full sunlight for a day, three days, or even
a week. The Sun's rays do the work here, burning away the unneces-
sary energies.
Place the stones in direct sunlight. An inside window ledge isn't
as good as an outdoor location because window glass blocks some of the Sun's rays. Remove the stones each day at dusk.
Some stones will be 'clear' after a day's soaking up the rays.
Others will need longer periods of time. Check the stones daily and
sense the energies within them by placing them in your receptive
hand. If the vibrations are regular, healthy, the cleansing has been
successful. A second method is somewhat more difficult. In this case, running water is the tool. Place the stones in moving water and leave them there for a day or two.
If you happen to have a river or stream running near your property, this is ideal. Place the stones in a net bag or devise some other
method to ensure that they don't wash away in the water. Leave them overnight in the water, which gently washes away the impurities.
The third main technique is governed by the powers of the Earth.
Bury the stone in the ground for a week or so, then check to see ifit has been purified. If it has, wash or wipe it off and your magic can
begin.
These are all natural purifications, performed with the energies
of the elements. If you can't do them, however, there is another
method, a ritual of purification, which can be performed in your own home. Perform this rite on your altar, if you have one, or on any table.
It is best done at sunrise or during the day.
Fill a basin with pure water and place thisto the West on the table
or altar.
Next, light a red candle and set this to the South. Light some
incense and place this to the East.
Finally, place a dish or flowerpot filled with freshly dug earth to
the North on the altar. In between all these objects set the stone to
be purified.
When all is readied, still your mind and pick up the stone in your
projective hand. Turn your attention toward the bowl of earth. Place
the stone on it and cover with fresh earth. Say something to the
effect of:
I purify you with Earth!
Leave the stone there for a few minutes, all the while visualizing
the earth absorbing the stone's impurities.
Then remove it, dust it clean, and hold it in the incense smoke.
Pass it nine times through the smoke, from the right to the left, saying
words like these:
I purify you with Air!
See the smoke wafting away the disturbing energies.Next, quickly pass the stone through the candle's flame several
times, saying:
I purify you with Fire!
The fire bums away all negativity.
Now place the stone in the water and say this or your own
words:
I purify you with Water!
Visualize the water washing it clean.
Leave the stone in the water for a time, then dry it with a clean
cloth and hold it in your receptive hand.
Is the stone'clean'? If not, repeat this simple ritual as many times
as necessary, until you are sure it has done its work.
Afterward, store the stone in a special place. It is ready for use
in magic.

Xandria makes excellent points. There are stones that should not be exposed to certain elements. Amethyst, fluorite, aquamarine and a few others will absolutely lighten if they are exposed for periods of sunlight. Selenite, gypsum, some feldspars should not be exposed to water as they will dissolve, I had a peice...golden butterfly selenite (i'll get a picture ofit eventually) that was in a bag that had leftovers from a chinese joint that it got exposed to so it had to be rinsed to get the sauce off...it absolutely changed the makeup of that stone and the shape. This aside there are some stones that NEVER require cleansing unless you are changing their intention that you laid upon them, selenite, black tourmaline, citrine to name a couple.

If you are not sure what the stone can handle for that, do a little research or ask here about that specific stone and one of us might know. Crystal magick!

I was just reading the healing techniques of Marcel Vogel. He originated the vogel cut healing wands, used to work for IBM and holds a bunch of patents for electronic stuff, magnetics and crystal systems. He recommended holding crystals between your thumb and index finger, setting your intention and blowing into each facet of the crystal/rock/gemstone. He was actually able to measure the energy difference between cleared and uncleared crystals using this technique. Obviously, you don't want to do that with a bunch of small crystals, but its good to know.