We haven't done Chuck E. Cheese, mostly becuase I think their pizza is terrible!
But, we have let DD play at McDonalds on occasion and she loves it. After our last visit there, I have had serious second thoughts about it, at least the local one we went to, because it was clear that the slides, tubes, and the floor had not been cleaned in some time!! The bottom of her socks were so disgustingly dirty that I just threw them away rather than try to wash them.
We have found a few indoor play areas for kids that do seem to be very clean and family-friendly, so we usually go to those instead.
Mom to 3 year old DD w/cf