I generally avoid anything less than a 3 hour connection time at EWR.

One time on a flight from BOS-EWR, which should be at worst a 45 minute flight, we spent an additional hour and a half circling over Northwest NJ. The guy sitting next to me who originally had booked with a 1 hr connection started realizing he was going to miss his once daily flight to Norway (from what I remember). Needless to say the FA didn't really know what was going to happen to him, and I was just thankful I wasn't in his position.