There are multiple ways of collecting each mote type which vary by element, but all of them drop off of certain Outlandmobs related to their element, specifically elementals of the related element.
A stack of 10 of any mote can be made into a Primal (of the same element), i.e. 10 [Mote of Water] → 1 [Primal Water]. The reverse conversion is not usually possible, but see Earth Shatter and Fire Sunder as exceptions.