Hi. John

The very common fungi can be used as biocides is the entomopathogenic fungi Beauveria bassiana  The entomopathogenic fungus Beauveria bassiana ((Balsamo), Phylum Ascomycota: Cordycipitaceae)  is a natural enemy of a wide range of insects and arachnids and have a cosmopolitan distribution. B. bassiana has been reported as a suppressive agent for several insect species worldwide, such as Helicoverpa armigera (Hübner), Alphitobius diaperinus (Panzer), Plutella xylostella (Linnaeus), Laniifera cyclades, Prostephanus truncatus (Horn), Polyphagotarsonemus latus (Banks) and Bemisia tabaci (Gennadius). B. bassiana has been extensively exploited as well for the field control of coffee berry borer, Hypothenamus hampei (Ferrari) in many countries around the world. Although first recognized as an insect pathogen, B. bassiana can exist endophytically in many wild and cultivated plant species . B. bassiana colonization of several herbaceous and woody species may provide  a degree of bio-protection to the hosts .The safety of B. bassiana as a biocontrol organism was evaluated based on impacts to nontarget insects and mammals including humans, and no safety concerns were identified (Zimmerman, 2007). There is a high potential for the use of Beauveria for biological control because such fungus can be cost-effectively mass-produced locally, and many strains are already commercially available. Also, B. bassiana has been mass produced on different solid substrates, including sugarcane wastes , silkworm pupal powder , agar medium and steamed rice Also, many companies used B. bassiana to produce different kinds.

Also, Trichoderma spp. is commonly used in biological control of foliar diseases, and used  in the integrated management.

You are best to choose species, which are commonly used in biocide testing regimes by various national and international organisations. However, I would suggest the following panel for consideration: Escherichia coli (Gram-negative microaerophile. Common GIT bacteria and occasional opportunistic pathogen), Pseudomonas aeruginosa (Gram-negative aerophile. Common environmental opportunistic pathogen and a type organism for antimicrobials resistance / tolerance studies), Staphylococcus aureus (Gram-positive aerophile. Common skin-associated bacteria with some pathogenic characteristics in some strains), Candida albicans (Pseudo-hyphal yeats. Common skin symbiont, but can convert to a pathogenic strain on some occasions) and Aspergillus niger (Common hyphal fungus. Sometimes associated with allergic reactions and rare pathogen). All of these organisms can be found as test organisms in the biocides literature.

John, 

For bacteria: 

1) you must take Enterobacteria: greateast choice - Escherichia coli (live in the intestines of healthy people  and reated to toxicogenic pathogens) and its close relative - Pectobacterium carotovorum (plant pathogen), Serratia marcescens, Pantoea agglomerns. all  can be opportunistic pathogens.

2) Bacillus cereus  - soil-dwelling, Gram-positive, beta hemolytic bacterium. Some strains are pathogens. Close relative of B. anthracis

3) Gamma-proteobacteria - Pseudomonas aeruginosa - common bacterium that can cause disease in animals & humans, close to large group of plant pathogens

4) Burkholderia cepacia  (beta group of proteobacteria) - related to many human and plant pathoges. Some strains are pathogens oh humans and plants too.

Next time I willl write about fungi

I support the choice of Dr. Collier on fungi:

Candida albicans and Aspergillus niger, plus you can take Fusarium species - they are toxicogenic, plant and human opportunistic pathogens. 

I will go with spp suggested by Peter. 

I recommend to work with reference strains such as E coli, P aeruginosa, S aureus, Bacillus subtilis Enterococcus, A. niger, Candida albicans purchased from recognized Culture Collections (for ex, ATCC). In this way the studies can be reproduced.

For fungi, I would select one that could be carried on people, like Aspergillus; and one common to air and buildings, like Cladosporium.

I recommend to work with reference strains such as E coli, P aeruginosa, S aureus, Bacillus subtilis Enterococcus, A. niger, Candida albicans purchased from recognized Culture Collections (for ex, ATCC). In this way the studies can be reproduced.

Unless you're anticipating sterilant efficacy, I'd not work with Bacillus spp.

ATCC 16404 is Asperglllus brasiliensis - A. niger is an obsolete name.