which output for cd s on 9000es?

To get the best sound from my 9000 do i use the digital or analog output for regular cd's?
Depends on what you are running it through. The SACD signal is only output through the analog outputs though.
I have been pretty disappointed with the D/A converters on the Sony. I've read a few reveiws that say just the opposite--use the analog out's when possible. I'm using a Levinson 36 D/A and although I don't use the Sony as a CD transport, I have tried it in this configuration. I don't think that's a terribly fair comparison, because the Levinson costs over 2x of the Sony. I still think my old Muse would outperform the Sony D/As--but I don't have it any longer so I can not give a direct comparison. As No-Money said--it depends on your D/A. Unless it is a very old, outdated, or poor quality D/A it is likely to best the Sony.
The 9000ES' DAC is probably equal to a $300 external DAC. I would not expect it to match a $3,000 Levinson DAC.

Several months ago, my 22 year old and I listened to several CDs to determine if we preferred the digital or analog outs. We prefer the analog outs, but it was close.

But I'm not a good test. I have a $2,000 Rotel 985 pre/pro. The analog outs feed into the 5.1 input and the signal stays analog.

With the digital input, the signal is converted to 24/48 in my Rotel, processed, and then converted to analog. There may be too many conversions which could be deleterious to the sound.