*Warning*This opinion might be controversial for some*
I know that it seems gross for your child to put things in his mouth and touch everything with germs on it, but honestly, he'll be fine. I am a firm believer that kids need to be exposed to a small amount of germs for their immune systems to function properly. When the body is exposed to germs it then makes antibodies-similar to a vaccine. Of course, be smart about it. Playing in the toilet is still a big no-no! :)
Besides, think about the big picture-- for all of human history babies and children have been playing in the dirt, touching questionable items and mouthing "dirty" items. Barring things like the Plague and other serious diseases, most kids have been fine.
To answer your question, I use my judgement on whether or not to clean a toy. If it's dirty as in dirt on it, I clean it, unless it's a sandbox toy. If it's been handled by a child who has a cold I clean it. Really, that's pretty much it. A completely sterile world is not healthy.
N.