What version of Debian are you using, and what are you trying to upgrade to. The xserver-9000 package is from Woody. Unless you need that package because you have a Weitek P9000-based graphics card, you can probably get rid of it with apt-get remove xserver-9000.
It's altogether possible that you can get rid of it even if you have that card. The newer xserver programs may support it natively.
At any rate, since you are evidently upgrading a very old system, I hope you have good backups.
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