Remember in the Velvetine Rabbit, how they just gather up all the toys and burn it all... Sounds like a darn good idea now, huh?!
Go through the toys and separate based on how you'll clean them. Things for the washing machine in one pile; things for bleach soak, another pile; things for clorox wipes, another... Use post it notes to mark large things you want to disinfect; when you've clean it, take of the post-it note. That way, you'll be able to keep track of what has and has not been gotten to.
You also want to check your water heater setting; to disinfect (stuffed animals, bedding, etc) the water temperature needs to be at least 170 degrees.
For clorine bleach, you ideally should use a container that has not be opened/unsealed longer than 30 days. That insures the concentration is the strongest. Dilute 1Tbls bleach for every gallon of water.
The reason I've never thrown toys in my dishwasher is because, if a toy were to melt, it would melt in my dishwater!! That could be a costly/annoying clean-up... And a smoke/fire hazard if the plastic melted onto the heating coil. So I always do it in the bathtub; surface spray toys with batteries. Used clorox wipes on book covers/pages, board games, etc.
And if you can afford it, you can always throw out popular toys that can be easily replaced with new ones. Of course, don't let your kid(s) know you're doing this... I've done this with various toys that are always at Target as well as just completely replacing crayons, markers, playdough.
If you think you'll get bleach drips on your carpet, you can always buy 2 brand new plastic garbage cans and do it outside.
When my daughter got Pertussis, I also had a steam carpet cleaning company clean rooms that she had been primarily in. Usually you can find an online coupon for 3 rooms for $99.
Here's an article that discusses disinfection aspects. Has good tips on remembering to clean light switches, faucets, door knobs, etc.:
http://www.michigan.gov/documents/Guidelines_for_Environm...