There have been at least 2 passing references to nanobots in Jimmy Neutron episodes that I am aware of. Perhaps my kids could refresh my memory- though I don't recall these references being altogether important to the plot. There was also one episode of Kim Possible involving a "nanotick" which was quite well done.
Hey, thanks, Eric,
I hadn't heard of the Kim Possible episode. I'll have to check it out.
Meanwhile, look at these!
'When Pants Attack'
Why the Nano Generation doesn't need us
Do you know where your children are?