It refers to the lettering on the old Disney ticket books. The letters helped determine the cost for an attraction (this was before it was a flat rate for everything). By the time EPCOT opened, the system was done away with. "A" was minor attractions, while "E" was attractions of grand scale. That's why you hear things like FJ, Transformers, Gringotts, etc referred to as E's.
These Days, Disney likes to exaggerate the definition of an E-ticket and likes to claim almost any "major" new addition is an E-ticket... including restaurants (not kidding). TSMM, Mermaid and Be Our Guest are recent examples of this.
Here are some examples (From 1959 Disneyland, but it at least shows where the term comes from):