The first question to ask is why do you feel it is necessary to disinfect or sanitize your diapers? Cloth diapers shouldn't have to be disinfected in normal circumstances.  Washing in a normal home laundering situation should clean diapers for normal usage.  The question of poopy diapers tends to come up at this point.  And my opinion is that breastfed baby poo is not going to be all that problematic it should be populated by "new, normal bacteria" according to webmd.  When a child's stools become more formed it is always recommended that the stools be removed prior to washing.  We will not be washing piles of poo in the washing machine.

Another important first step is to determine what you are trying to sanitize your diapers from.  Are you dealing with a fungal yeast infection? bacterial or viral infection in the family? precaution after accepting childhood vaccinations? or what if your family is dealing with MRSA? Each of these scenarios will probably prompt slightly different methods of sanitizing.

Historically to eliminate germs from laundry people would boil clothing and hang items outside to dry in the sun.   These methods would conceivably work in the modern age but may not always be feasible.  Particular concern would be risen for boiling.  While boiling prefolds may work, many modern diapers and fabrics would not be suitable for boiling.  Also boiling would be rigorous, messy, and potentially dangerous.

Ultra Violet Light: Sun drying allows the UV rays of the sun to irradiate germs.  The efficacy of sun drying isn't reported that I know of, and the ability to sun dry is limited by weather conditions and homeowner associations.  The homeowner associations need to get a green makeover, but there is not much you can do in a rainy season.  In the winter, line drying is still an option if you are willing to brave the cold.  Items will dry, UV rays are actually stronger.  Another option may be to sun in a window or dashboard of your car.  Realize that this type of sunning will take longer and less UV rays will be penetrating the glass.  UV Rays of the sun work effectively against viruses, bacteria, germs, mold, dust mites and flea eggs.  UV rays are ineffective against killing yeast.  A new product has recently been introduced to mimic the suns UV rays called the CleanWave UV-C Sanitizing Light Wand. Essentially it is a wand that can be waved over surfaces for cleaning.

Hot Water: Laundry that may be contaminated is most often advised to wash with detergent in hot water of 135-145 degrees Fahrenheit some sources recommend 180 degrees Fahrenheit.  Hot washing may be best followed up by drying on a hot dryer setting. Yeast will effectively be killed at temperatures above 122 degrees Farenheit.  You may need to turn your water heater up prior to laundry, if so be careful to restore the temperature to safe levels after washing.

Chlorine Bleach (Sodium Hypochlorite Bleach): is one of the most common forms for disinfecting laundry.  With all the varieties of bleach on the market today be sure to check the label for the one that kills germs. Not all are rated for germ killing.  Diapers should be washed free of any poo before chlorine bleach is used since feces can inactivate its disinfectant properties.  Chlorine Bleach is effective against fungi (yeast), bacteria and algae but not spores.  Chlorine bleach is considered most effective when used with cold water.  Chlorine bleach can harm stainless steel washer drums so check with your washers manufacturer before use if you have a stainless steel washing drum.

Oxygenated Bleaches/Non Chlorine Bleach (Sodium Percarbonate): is effective against bacteria and fungal yeast, and can be used at lower temperatures but is considered " more effective when used in hot water 130 degrees."⁽²⁾  Concentrations for effective disinfecting are not documented. Some of these products are loaded with other additives.  We suggest you read your labels well and find one without fillers and fragrance and that has a high percentage of Sodium Percarbonate.  Seventh Generation makes a product that looks good.

Stabilized Hydrogen Peroxide: effective against viruses, vegetative bacteria, fungi and bacterial spores.  Concentrations for effectiveness are not documented.

Pine Oil Cleaners: I can't seem to find much information on using this with laundry except that it can be done and it is considered a disinfectant.  Our mothers and grandmothers could have used it in our wet diaper pails instead of chlorine bleach.  One thing that does pop up on it is its ability to aggravate asthma. 

Ammonia: Compromised by use in hard water.  Is not effective against some viruses, fungi, and bacterial spores.

Natural Enzymes: Useful as stain removers and are very selective to the type of stains per the type of enzyme.  Research in this area is still new but here is what I have gathered protease enzymes would be used against bacteria. Both protease enzymes and cellulases enzymes would be needed for combating yeast.  The use of enzymes alone may not be enough to sufficiently eliminate either bacteria or yeast in laundering. (Protease is the same group of enzymes though that attack protein and could cause skin issues if left in the fabric.)

Vinegar: Effective as a mild antibacterial agent for hard surface cleaning, but is not effective against fungus such as yeast. It can also dissolve mineral deposits from hard surfaces. Curiously vinegar can be used as a yeast enhancer in baking bread and it seems to reason that it could actually promote a faster yeast growth in laundry. As far as bacteria vinegar seems to perform well here is an easy article.  (There are old school suggestions for using vinegar against yeast by putting vinegar in the final rinse cycle and then drying in the high heat of the dryer.  The concept behind this is that the vinegar would attack the outer sheath of the yeast and make it more susceptible to death from the dryer heat.  I couldn't find any research that would support this process though.)

Apple Cider Vinegar: Effective as a mild antibacterial agent for hard surface cleaning, but is not effective against fungus such as yeast. Curiously vinegar can be used as a yeast enhancer in baking bread and it seems to reason that it could actually promote a faster yeast growth in laundry.

Grapefruit Seed Extract: Seems to be a good choice when dealing with a yeast infection and should be effective against bacteria as well.  Here is an easy read article along with directions for use when dealing with yeast.

Tea Tree Oil: Is considered antibacterial and antifungal. Care should be used for proper use since high concentrations can harm the skin.  When purchasing do choose a good grade with ingredients listed at least 35% Terpinen 4-ol and less than 10% Cineole. Again I can't find an easy to read article describing the how of using tea tree oil for disinfecting laundry.  For use topically you should mix the essential oil with at  least two tablespoons of oil like olive or coconut before applying.  Of course their is the concern regarding potential estrogenic effects from the Tea tree oil. So do some research if this is the route you want to go.  I know some people have used this in the wash.  I wonder about its efficacy when used in a large tub of water.  Also it has been reported to cause issues with the modern synthetic diapers.

Colloidal Silver: is not tested by the FDA but claims exist that it will prevent the growth of bacteria, fungus and viruses. Its suggested usage is in the final rinse water.  Again how much would be needed in the final rinse for effectively disinfecting diapers is not known.

²  http://www.cleaning101.com/laundry/fact/fact_sheet3.html