I've had both modded by Dan, the 999ES modded to the hilt with the clock, and a bon-mod 9000ES, also with the clock. I kept the 9000es as it easily bettered the 999es. It presents music in a much more organic, real way. It is also sturdier and heavier than the 999, and much better shielded.
The 9000es will play CD-Rs, as I have found that Maxell's MusicPro CD-Rs work in it.