For some reason, selecting preferences in Safari 3.0.4 only shows the tabs preference pane. I can't even see the others to select. Have a look at the attached screenshot to see what I mean.
try deleting your user Cache folder in home/Library/ (dont worry it wont hurt anything) and dragging the com.apple.Safari.plist preference file in home/Library/Preferences to the desktop and rebooting.
the Safari preference file holds all the settings you made in Safari's preferences. if this doesnt work or deleting the Cache folder did drag it back to the Preferences folder so you get your settings back.