As before, you'll want to open the NSPrefPaneGroups.plist file,
/Applications/System Preferences.app/Contents/Resources. As before, you'll see a number of different groups. But unlike in Jaguar, the names of these groups do not correspond to the names they have in the System Preferences window; this is because they are localized strings. If you want to change the name of one of these groups (say, "Other" to "Third-Party"), you'll need to instead edit the Localizable.strings file in the "English.lproj" (or insert your language here.lproj) subdirectory of Resources.

If you want to add more groups, you could go back to the Localizable.strings file and add a new mapping, but a more straightforward way is just to enclose it in double-quotes in the NSPrefPaneGroups.plist file (strictly speaking, even the double-quotes probably aren't necessary, and indeed if you're editing this within PropertyListEditor you can just add the group name as usual, but it's probably good convention to explicitly specify that this is a literal string.)

Now, the tricky part is adding new preference panes to the individual groups. Since the internal identifier for each pane is no longer in the NSPrefPaneGroups.plist file by default, you'll need to go find them in each third-party pane you wish to add. The string you want is the NSBundleIdentifier which is stored in the Info.plist file in the Contents folder within the package for each preference pane. This might not look like the strings for the default Apple panes; FruitMenu's is "com.unsanity.fruitmenu.editor", but APE Manager's is just "APE_ManagerPref". In any event, add it to the appropriate group (be careful if you're working manually in a text editor: don't forget about the commas at the end of each line!) and then save it. You'll probably have to perform a Save As... and save it to the Desktop, then use the Terminal to copy it to the correct location.

After all that, just open System Preferences and you should see the changes.