Standard Process Identification of New Disease outbreak Causing Pathogen
I was first thinking of voting to close the question because it was too broad, but in reconsideration I think the answer of showing why it is too broad would constitute a proper answer in this case.

First of all, the term disease is one of the most general terms for a problem in medicine.  The only term that could be higher up is "medical condition."  It could be an infectious disease, genetic disease, induced disease (think chemicals, tobacco, etc), or [insert organ here, ie heart] disease (which are not necessarily genetic).  There are attempts to distinguish between "diseases" and "disorders," but the difference is not always clear.  The term "disorder" is growing in usage and scope because it is seen as having fewer negative connotations than disease (think disease of the mind vs. disorder of the mind).

Thus each field has it's own ways of identifying new diseases.  As a general trend new diseases are found now by identifying greater specificity within a previously general disease.  For example, a person could be said to have an "adrenal cancer," but now we would want to know if they have an adrenocortical carcinoma.  In an infectious setting, we could think of all the particular pneumonia being specified out of interstitial lung diseases.

Diseases caused by external agents (pathogens, toxins, etc) can sometimes be more uniquely novel, in that they can change into something unpredicted (new compound or virus made by man for example).  Perhaps you meant to ask if there were standard ways for identifying new viruses or microbes?