I run the plush toys through the wash, and then dry them for a few minutes, then let air dry. If some of them don't make it through the cycles, they get tossed out. I can get them pretty cheap on clearance at Target and from PetEdge, and we got like a MILLION from the last GE

so it's ok to retire the ones that fall apart.
I run the hard toys & kongs through the dishwasher on a sanitize cycle.