Gamespot confirms that other names missing from the list – Bethesda, id Software, Majesco, and D3Publisher – still plan on attending. Kotaku claims that id Software is not attending despite Gamespot's story to the contrary. We've contacted id for clarification. They also assert that Her Interactive (best known for their popular Nancy Drew games) won't be attending, though the publisher didn't attend E3 last year either. We reached out to peripheral manufacturer Nyko who said that, though they aren't listed on the official site, they will nevertheless be attending.
As for a specific reason for the absences, outside of timing and exposure, Kotaku cites several unnamed sources who pin the blame straight on current ESA pres Michael Gallagher's well-tailored lapel. Is Gallagher out of touch with the video game industry?
[Update 4:58pm: Added Atlus and Nyko details.]
Read – Activision/Vivendi leave ESA, skip E3
Read – Five Publishers Drop Out of E3 This Year, Some Blame ESA President
Read – NCsoft, Foundation 9 bypass E3 '08