In order to access the ROMs, you will need to download and perform the following.

• Download the release build of the Cowabunga project from here[github.com] under the assets section of the most recent version. Right Click the download and click "Extract All" to extract the files in the downloaded archive.
  
• Copy the Executable "cowabunga64.exe" in the extracted folder to the Game's Directory.
  
• Run the command prompt by going to the address bar in the file explorer and typing "cmd" and pressing enter.
  
• Enter the command "cowabunga64.exe -k cowabunga assets.pie assets.zip"
  
• Wait for the program to finish, it will be complete when you are able to enter text in the command prompt again.
  
• A new zip file will be created in the Game's Directory titled "assets.zip". Right Click and click "Extract All" or double click it to enter it.
  
• Go to the "roms" folder inside the archive/extracted folder.
  
• The roms are in the newly made and aptly titled folders based on the console they appeared on.

This one is more complicated. The ROMs in the folders are unfortunately not in the correct format.

• First you will need to download the "tmnt-cc-arcade-extract.sh" file[github.com]. Place the downloaded "tmnt-cc-arcade-extract.sh" in the same directory as the "TeenageMutantNinjaTurtles" and the "TeenageMutantNinjaTurtles2".
  
• Download the "ts_rom_tool.py" dependency[github.com]. Place the downloaded "ts_rom_tool.py" in the same directory as the "TeenageMutantNinjaTurtles" and the "TeenageMutantNinjaTurtles2".
  
• Download and setup Linux on Windows
  
  • Method 1: Download the following from the Windows App Store:
    
    • Windows Store "Windows Subsystem for Linux" Download Page.[www.microsoft.com]
      
    • Windows Store "Ubuntu for Windows" Download Page.[www.microsoft.com]
      
    • Restart your computer after installing both.
      
  • Method 2: Follow the following guides:
    
    • Windows Subsystem for Linux Setup Guide.[www.thewindowsclub.com]
      
    • Ubuntu for Windows Setup Guide.[learn.microsoft.com]
      
• Navigate to the Konami folder and the four items inside. Open the command prompt in that directory by going to the address bar in the top, "cmd"and pressing enter on the keyboard.
  
• Enter and run the command "wsl sudo apt install zip" to install a needed dependency. Press "y" to confirm the installation when prompted.
  
• Next, in the command prompt, enter the command "bash tmnt-cc-arcade-extract.sh".
  
• You should then be presented with three .zip files. all of which can be launched using MAME.

NOTE: These ROMs are specifically for MAME, not Final Burn Alpha / Neo.

File Name
Game (DO NOT CHANGE THE FILE NAME OR EXTENSION)
Important Notes
tmnt.zip
Teenage Mutant Ninja Turtles (World 4 Players, version X)
This was modified to remove its original title theme song, so the intro and attract mode don't have any music in them.
tmntj.zip
Teenage Mutant Ninja Turtles (Japan 4 Players, version 2)
This was modified to remove its original title theme song, so the intro and attract mode don't have any music in them.
tmnt2.zip
Teenage Mutant Ninja Turtles - Turtles in Time (4 Players ver. UAA)
Extra Dash Button from The Cowabunga Collection may not be included.

Here are all the items with their proper names in the Nintendo Folder.

The Game Boy folder has some specialized BIOS bin files as listed below.

ROM Title
What it Is
Notes
agb_boot.bin
Game Boy Color Boot ROM used in the Game Boy Advance's Game Boy Color mode
Very few emulators use this.
cgb_boot.bin
Game Boy Color Boot ROM
It is a useful BIOS for emulation in, for example SameBoy.[docs.libretro.com]
cgb_boot_fast.bin
A modified version of the Game Boy Color Boot ROM that skips the intro logo
Not recommended to be used for emulation BIOS.
dmg_boot.bin
Original Game Boy Boot ROM
It is useful BIOS for emulation in, for example SameBoy.[docs.libretro.com]
sgb_boot.bin
Super Game Boy CPU Boot ROM
It is useful BIOS for emulation in, for example Mesen-S.[docs.libretro.com]Note that this is not the Super Game Boy ROM, which would be needed as well.
sgb2_boot.bin
Super Game Boy 2 CPU Boot ROM
It is useful BIOS for emulation in, for example Mesen-S.[docs.libretro.com]Note that this is not the Super Game Boy 2 ROM, which would be needed as well.

And here is the Game ROMs.

File Name
Proper File Name (With Correct File Extension)
Notes
Teenage Mutant Ninja Turtles - Fall of the Foot Clan (USA).bin
Teenage Mutant Ninja Turtles - Fall of the Foot Clan (USA) (Cowabunga Collection, The).gb
Teenage Mutant Ninja Turtles (Japan).bin
Teenage Mutant Ninja Turtles (Japan) (Cowabunga Collection, The).gb
Teenage Mutant Ninja Turtles 2 (Japan).bin
Teenage Mutant Ninja Turtles 2 (Japan) (Cowabunga Collection, The).gb
Teenage Mutant Ninja Turtles 3 - Turtles Kikiippatsu (Japan).bin
Teenage Mutant Ninja Turtles 3 - Turtles Kikiippatsu (Japan) (Cowabunga Collection, The).gb
Teenage Mutant Ninja Turtles II - Back from the Sewers (USA).bin
Teenage Mutant Ninja Turtles II - Back from the Sewers (USA) (Cowabunga Collection, The).gb
Teenage Mutant Ninja Turtles III - Radical Rescue (USA).bin
Teenage Mutant Ninja Turtles III - Radical Rescue (USA) (Cowabunga Collection, The).gb
The Map icons use the improved versions from the Japanese release.

The NES folder has Nintendo Entertainment System and Nintendo Family Computer ROMs in the ".bin" format.

File Name
Proper File Name (With Correct File Extension)
Notes
Geki Kame Ninja Den (Japan).bin
Gekikame Ninja Den (Japan) (Cowabunga Collection, The).nes
Teenage Mutant Ninja Turtles (USA).bin
Teenage Mutant Ninja Turtles (USA) (Cowabunga Collection, The).nes
Teenage Mutant Ninja Turtles (Japan).bin
Teenage Mutant Ninja Turtles (Japan) (Cowabunga Collection, The).nes
Teenage Mutant Ninja Turtles II - The Arcade Game (USA).bin
Teenage Mutant Ninja Turtles II - The Arcade Game (USA) (Cowabunga Collection, The).nes
Modified to use the Improved Jump Kick from the Japanese version.
Teenage Mutant Ninja Turtles II - The Manhattan Project (Japan).bin
Teenage Mutant Ninja Turtles 2 - The Manhattan Project (Japan) (Cowabunga Collection, The).nes
Teenage Mutant Ninja Turtles III - The Manhattan Project (USA).bin
Teenage Mutant Ninja Turtles III - The Manhattan Project (USA) (Cowabunga Collection, The).nes
Teenage Mutant Ninja Turtles - Tournament Fighters (USA).bin
Teenage Mutant Ninja Turtles - Tournament Fighters (USA) (Cowabunga Collection, The).nes
Playable bosses may not be unlockable like in the Cowabunga Collection.

The SNES folder has Super Nintendo Entertainment System and Super Family Computer ROMs.

File Name
Proper File Name (With Correct File Extension)
Notes
Teenage Mutant Ninja Turtles - Mutant Warriors (Japan).bin
Teenage Mutant Ninja Turtles - Mutant Warriors (Japan) (The Cowabunga Collection).sfc
Teenage Mutant Ninja Turtles - Tournament Fighters (USA).bin
Teenage Mutant Ninja Turtles - Tournament Fighters (USA) (The Cowabunga Collection).sfc
Playable bosses may not be unlockable like in the Cowabunga Collection.
Teenage Mutant Ninja Turtles - Turtles in Time (Japan).bin
Teenage Mutant Ninja Turtles IV - Turtles in Time (Japan) (The Cowabunga Collection).sfc
Extra Dash button inlcuded in the Cowabung Collection isn't included. Also, the Controls option to map Special Moves to a single button was removed from the ROM.
Teenage Mutant Ninja Turtles IV - Turtles in Time (USA).bin
Teenage Mutant Ninja Turtles IV - Turtles in Time (USA) (The Cowabunga Collection).sfc
Extra Dash button inlcuded in the Cowabung Collection isn't included. Also, the Controls option to map Special Moves to a single button was removed from the ROM.

The Genesis folder contains ROMs for the SEGA Genesis and SEGA Megadrive.

File Name
Proper File Name (With Correct File Extension)
Notes
Teenage Mutant Ninja Turtles - Tournament Fighters (U) [c][_].bin
Teenage Mutant Ninja Turtles - Tournament Fighters (USA) (Cowabunga Collection, The).md
Playable bosses may not be unlockable like in the Cowabunga Collection.
Teenage Mutant Ninja Turtles - Tournament Fighters (J) [_].bin
Teenage Mutant Ninja Turtles - Tournament Fighters (Japan) (En) (Cowabunga Collection, The).md
Playable bosses may not be unlockable like in the Cowabunga Collection.
Teenage Mutant Ninja Turtles - The Hyperstone Heist (U) [_].bin
Teenage Mutant Ninja Turtles - The Hyperstone Heist (USA) (Cowabunga Collection, The).md
Teenage Mutant Ninja Turtles - Return of the Shredder (J) [_].bin
Teenage Mutant Ninja Turtles - Return of the Shredder (Japan) (Cowabunga Collection, The).md

Thanks to

• Teamopolis for the Table Generator for making this guide easier to make.[www.teamopolis.com]
  
• Masquerade64 for his Cowabunga Github Project[github.com]
  
• RED-Project for continuing their work to make all the Emulated Game Collections ROMs' dumpable for emulation.[github.com]
  
• This Steam Discussion Post indicating the various differences between the original and Cowabunga Collection differences.