As was previously mentioned, you should cleanse your stones before too but especially after every time that you use them. This page contains some ideas as to how to go about cleansing your Stones for use.
Not all of these ideas belong to the creator of this page, many were contributed by other experienced Witches. Their names shall preceed their contribution.

A good and easy way to cleanse your stone is using water, either in a stream or brook or river (if you have access), or using rain water that you collect during times when it rains outside, or even using tap water and just envision it as being in a stream, under a waterfall, whatever you desire.

"When I first get a stone I first wash it in blessed sea salt, then sleep with it in my pillow for about a month to 'charge it' with my energy. To cleanse it, again it goes into sea salt. You can also 'smudge' them."

"When I get a New crystal, I wash it in Element Water. Element water is water captured in a vessel during a thunder & lightening storm. It is pretty powerful stuff. I also leave it in this water and put it on a sill in the moonlight. Then, I take it from there, and put it in running water in the sunlight. Rivers, streams, whatever, as long as it's running. I have heard of cleansing them in fire, and water, also smudging. Myself, I do a lot of washing, and asking Mother to bless it to my purpose."

Peg also says:

"When I'm out of element water, I use Kosher salt to make brine, as close to ocean water as I can get. I also use sea salt when I can get it. These work very well. When I get to a spot I can settle in for a bit, and it has a good storm, I'll gather element water again, and send it out. When I was in the mountains, I used the Earth to clean crystals. A virgin spot that I could smell the Earth in, that was rich and loamy. I have also left them out 24 hours in the sunlight & moonlight so all energies from before are gone from it. I still feel running water is still the best."

#1:
"This is the one I use most often. Take a small jar, and place sea salt in it. Whenever you buy a new stone or feel that a stone has to be cleansed you simply shove it into the jar. You can shake the jar to make sure that it is covered in the salt. Now place the jar in a window where it will receive both sun and moon light. You now leave it to sit until it calls to you. What I mean here is that you will be drawn back to the stone. At this time you will remove the gem from the jar with the salt and you will wash it in running water. Tap water works for this as well as any other kind. Now place the stone back in the window to re-charge the stone. It will sit overnight or about a 24 hour period."

#2:
"Take the stone and bury it beneath a mud puddle. After the puddle has dried up, remove the stone and charge it. In this fashion the earth itself absorbs all the negative energies from the stone."

#3:
"Wash your stone in any kind of moving water. This can be a lake that has a wave, a river, or tap water, or whatever is available. As you wash the stone you will visualize all the negative energies leaving the stone and being washed away from it, flowing with the water, out and away. Once more you need to charge the stone after the cleansing process is over."