In the hopes that Battle for Naboo might someday be brought to GOG, here is a registry edit that allows Battle for Naboo to run on 64-bit versions of windows. To get this to work:

1) Copy and paste everything inside the five dashes to a blank text file in notepad.
2) Change all of the path names to match your system (if your CD drive is drive D, change CD Path to "E:" . If your game is installed in the C drive, change all of my "D:\\" references to "C:\\" .
3) Change your desired resolution in the "Screen" field to match your PC. It is possible to put in a widescreen resolution instead of 4:3 aspect ratio in this field.
4) Save the document as BFN.reg and place in your "Battle for Naboo" folder
5) Right click the BFN.reg file, and select merge to add the key to the registry

Afterwards, you should be able to run the game from the executable file under Battle For Naboo/data_pc/BFN.exe

There is an executable out there edited to allow the game to run without a disk, though I prefer to mount the burned iso of my old CD to a virtual drive these days.

You can still change game options with the BattleForNaboo.exe file in the main Battle For Naboo folder, though this will reset the screen size and lock to a 4:3 resolution until the registry key is updated again.

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Windows Registry Editor Version 5.00

[HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\LucasArts Entertainment Company LLC\Battle for Naboo\Retail]
"Analyze Path"="D:\\Games\\Battle for Naboo\\Install\\SysCheck.exe"
"CD Path"="E:"
"Executable"="D:\\Games\\Battle for Naboo\\data_pc\\BFN.exe"
"Install Path"="D:\\Games\\Battle for Naboo"
"Launcher"="D:\\Games\\Battle for Naboo\\BattleForNaboo.exe"
"Source Dir"="D:\\"
"Source Path"="D:"
"UninstallString"="C:\\Windows\\uninst.exe -f\"D:\\Games\\Battle for Naboo\\Install\\DeIsL1.isu\" -c\"D:\\Games\\Battle for Naboo\\Install\\LecSetup.dll\""
"InstallType"=dword:00000001
"Installed"=dword:00000002
"Registration"=dword:00000002
"Screen"="2736x1824 (32 bit)"
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Assertion Failed: "clt_IsDirectoryPresent(g_ENV[*dataDir"])"!

File C:\cws\cpp\BFN\Source\LFX_system.cpp
line 170