I think you should head over to www.audioasylum.com. They have done unthinkable numbers of threads on this topic, and searching their archives will lead to very thorough responses.
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Musically, the 9000ES is superior in most areas, has superior build, transport, shielding. If you can do without the multichannel hype, it's a no-brainer.
Go back a couple of issues of Absolute sound and find the review of the NS999ES. There are many comparative notes between it and the 9000ES.
I echo juaudio and encourage you to read the Absolute Sound from one or two back issues ago because the review of the NS999ES was pretty much an endorsement of the S9000ES. The latter is an outstanding SACD (stereo only) and, surprisingly, a phenomenonal redbook CD player. Unfortunately, it's only an moderate performing DVD player. However, you'll read on audioreview.com high praise for it as a DVD player. I was fortunate enough to come across a S9000ES this past spring as a demo/close-out and got a great deal so I wish you well in finding a used one. I use my S9000ES for redbook CDs and SACD but I use a Denon DVD player for my video.
Deciding between the two Sonys depends on your needs. If you want an introduction to stereo SACD and an outstanding redbook CD (which you likely have many of), the S9000ES is the way to go. However, if you want multichannel SACD and outstanding DVD video, you'll get a slightly compromised package in the NS999ES.
As a wise one pointed out to me, "There are no perfect answers in life, just better or worse options." You might want to explore other options depending on your needs.
Nothing really new to add here - agree the 9000ES is better built than the 999, but lacks mulit-channel SACD playback (who cares?). Disagree with Jwong1 that CD playback is "outstanding". To the contrary, in my two plus years of owning this player, redbook CD playback is average at best even with the digital circuits switched off. I use this player for DVD playback only.
Also disagree that video playback is only "moderate performing". The 9000ES is still the reference player in many print reviewer's systems. The picture quality is quite good using Transparent S-Video cables and even better running component out.
Finally, there are plenty of used 9000ES listed on audiogon from time to time at around $800. You might also consider the new Phillips 963 at $500 retail. It is also getting rave reviews. Good luck!