You must put energy into your mala before counting recitations with it, to produce real benefit.
I interpret this as cleansing and blessing the mala before use.
Coil the mala in your upturned right palm and cup your left palm over the top.
Recite 'Om Ah Hum' 7 times whilst rubbing the mala beads between the hands.
Then blow gently into the mala 3 times.
If you have an HYT Yidam then use their mantra for the 7 repetitions and use 'Om Ah Hum' each of the three times you blow into it.
There are variations of course. I've seen a Geshe additionally recite 7 mantras, counting them on the mala in the traditional way.
I've seen others simply use the three breaths whilst rubbing the mala at the same time.
I'm sure there are other ways such as leaving the mala on the shrine for a while, and new agey or cultural methods using blessed water, a pyramid crystal, etc.
The material used is also considered important. Bodhiseed is considered suitable for all purposes. As an example of other materials, some belelieve that a lapis mala used for Medicine Buddha practice will become blessed through the practice and the energy in it may be used for healing by placing the mala on a patient.
Energising in other faiths is also performed. In the case of a Hindu, the process may be somewhat long and complex:http://www.astromandir.com/rud2.html