One way to cleanse your crystals is to hold them under running water. As you do so, ask the Universe to remove all of its negativity. I usually imagine a ray of white light around the stone as I do this, cleaning it and filling it with wisdom & positive healing energy. 

Certain crystals associated with purification like carnelian and clear quartz are thought to actually cleanse other stones. Stack these stones on top of any crystals that need clearing, or keep them all in the same bag when you travel.

Another option is to leave your crystals outside or on a windowsill during a full moon so they can bask in the cleansing energies of the moon. But don't stress if you forget; the moon's energy will stick around for about three days, so you have a window of time each month to get those crystals of yours cleaned up. All you need to do is leave them out, and your intuition will tell you when they're all charged up. Easy!

NOTE: Stones that can't get wet include:  Calcite, Kyanite, Kunzite, Angelite, Azurite, Selenite, Fluorite (especially SALT water) Many of these crystals will completely dissolve when place in water, or they will lose their shine. Either way, play it safe when it comes to these minerals and ALWAYS DYOR (do your own research).

How to program your crystals