When I updated to 10.4, I realized I hadn't used Classic for a very long time. I wanted to remove it, and prevent the Classic System Preferences pane from appearing. Lots of hints describe messing with the system parts to do this, but it felt pretty untidy to me, so here's what I did.
You can't simply trash the System Folder that is used for OS 9, as a booted OS X won't let you -- it says it's in use. I rebooted in single user mode (hold Command-S at startup), mounted the drive writable and removed it that way. Once at the singleuser prompt, do
$ mount -uw /
$ cd /
$ rm -rf 'System Folder'
Be very careful with your spaces and escapes, or it's bye-bye to the /System folder (the actual OS X folder!), which would be very bad.
Now you can reboot and remove /Applications (Mac OS 9) from your disk -- the Finder lets you do this just fine. Now to fix things up so that the Preferences pane doesn't appear, and the system doesn't think there's an OS 9 bootable part of the disk. In the Terminal, do:
$ sudo bless -folder /System/Library/CoreServices
Thiss will re-bless the OS X folder, and remove any blessing from the now-removed OS 9 folder. You will also need to find the com.apple.Classic.some_number.plist file in ~/Library/Preferences/ByHost/, and remove it:
$ rm ~/Library/Preferences/ByHost/com.apple.Classic.some_number.plist
If there is a file at ~/Library/Preferences/ called com.apple.Classic.plist, remove that, too. Additionally, there may be a folder at ~/Library/Classic containing a file called .LoadClassicPref. That should be deleted, too, after checking that there's nothing in the folder you want to keep:
$ rm -rf ~/Library/Classic
You may wish to repeat the above preference removals for all users.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050430120117382