I'm more scared of little bugs that think they can live with me.
Where I grew up, it was not someone was "the Cootie"; it was so-and-so HAD the cootieS. Seems to me that this originated in that particularly nasty brand of schoolyard bullying in which the whole group turns on some poor kid and ridicules him/her because of perceived shortcomings in his/her family background. By my day, I don't think any kids (in my school) actually knew what cooties were; "So-and-so has the cooties!" had become a pretty innocuous taunt.
I don't have any examples off the top of my non-infested head, but I think you could find examples of real-live bogey-men referenced in children's games from the past. Anyone know of any?
It used to be accepted wisdom that Ring Around the Rosy was about the plague, but apparently that notion has been debunked ...