I have OS X on a separate partition, these are all the os x Jaguar files installed on this partition. Trash them all...but be careful not to trash the OS 9 system.
code:
. Desktop DF cores
.. Desktop Folder dev
.DS_Store Developer etc
.Trashes Icon? mach
.VolumeIcon.icns Library mach.sym
.audacity_temp Network mach_kernel
.hidden Pictures misc
.journal System private
.journal_info_block TheFindByContentFolder sbin
.vol TheVolumeSettingsFolder sw
AppleShare PDS Trash tmp
Applications Users usr
Desktop Volumes var
Desktop (Mac OS 9) automount
Desktop DB bin
The files with the period or "dot" ( . ) are invisible in OS X, they may be invisible in 9 as well (I can't remember).
All the files and folders listed above are OS X and can be safely trashed, but backup anything of value in your user folder( /Users/user-name/ ) and Applications folder.