Well, I'm not altogether sure what you mean by the "key method" of classifying organisms. I performed a search and was unable to come up with anything even remotely referring to a key method used in the classification of organisms, so I shall assume you are talking about the current practice of Linnaen Taxonomy, whereby organisms are grouped according to kingdoms, phylums, groups, and subgroups.
There are several different ways one could organize organisms. One would be the location, geographically speaking, of the organisms. Organism population location exists for a reason; there are conditions in place that lend themselves to fostering a home base for a group of organisms for a reason.
Another method I would employ in classifying organisms into groups would be social behavior. Not all organisms work well in group settings. Then again, not all organisms work well by themselves. How the organism relates to other members of his species, whether there is an established system of rules, would be worthy of categorical consideration.
Third, I would recommend life span, or how long an organism's average life expectancy is. It has always been a source of amazement to me that a fruit fly's entire lifespan is only a few days, compared to a bristlecone pine tree that can have a lifespan for hundreds of years, if not a thousand years! There is a huge spectrum to be examined in terms of life span, and how that relates to other members of a group of organisms.