Tray folder and mods folder

While you can't use sub-folders inside the Tray folder, it's possible to instead move the contents of the Tray folder inside the Mods folder, and use sub-folders there.

To do that, edit your Resource.cfg file inside the Mods folder and add the following lines:

DirectoryFiles Tray autoupdate
DirectoryFiles Tray\* autoupdate
FileType 0x2a8a5e22 trayitem
FileType 0x3924de26 blueprint
FileType 0xd33c281e bpi
FileType 0xb3c438f0 householdbinary
FileType 0x3bd45407 hhi
FileType 0x56278554 sgi
FileType 0x370efd6e room
FileType 0x00de5ac5 rmi

Then create a Tray folder inside your Mods folder, and move whichever files you want to organize into sub-folders inside that newly created Tray folder.

I don't think it's supported, though. I recommend not trying to delete from inside the game anything you move to the Mods/Tray folder, last time I tried it crashed the game, but apart from that this is working just fine for me.

If you know your way around creating .package files, the above info can also be used to pack lots, households, and rooms inside .package files.

Edit: Testing a bit more, it seems like rooms don't work. They appear on the Gallery, but behave as if the .room file isn't there. Either the game somehow prevents .room files from being loaded from outside the Tray folder, or else I got the filetype wrong. Households and lots seem to be working fine, though, as I was able to place lots and households I've moved to the Mods folder.