Pre-requisites:

VC++ 2017 x86 Runtime Libraries
Node.js x86 Libraries

1.) Download the latest zip.
2.) Extract the zip file.
3.) Run modloader64-gui.exe to run the first time update and to populate folders.
4.) Download OotOnline.pak (Mod)MischiefMakersOnline.pak (Mod)MajorasMask.pak (Core)MajorasMaskOnline.pak (Mod).
5.) Move mod .paks to ./ModLoader/mods/ and core .paks to ./ModLoader/cores/
6.) Congratulations, you have installed ModLoader64!

Video Tutorial

Installer Script (Debian and Red Hat based Distros)

Pre-requisite: curl

1.) Download the installer script and extract all contents.
2.) Open a terminal and navigate to the downloaded script.
3.) Run ./install.sh in the terminal to start the installer. (DO NOT RUN AS SUDO/ROOT)
4.) Follow the prompts and select your package manager to install.
5.) Download OotOnline.pak (Mod)SuperMario64.pak (Core)Sm64Online.pak (Mod)MischiefMakersOnline.pak (Mod)MajorasMask.pak (Core)MajorasMaskOnline.pak (Mod).
Folders will be located as follows:
Roms: /opt/modloader64-gui/ModLoader/roms/
Mods: /opt/modloader64-gui/ModLoader/mods/
Cores: /opt/modloader64-gui/ModLoader/cores/
6.) Run ModLoader64 via your applications menu.
7.) Congratulations, you have installed ModLoader64!

Manual Install

Pre-requisites (apt): libglew2.1 libsdl2-ttf-2.0-0 libsdl2-image-2.0-0 libsdl2-mixer-2.0-0 libsfml-system2.5 libsfml-audio2.5
Pre-requisites (yum): libGLEW.i686 libGLEW.x86_64 SDL2_ttf.i686 SDL2_ttf.x86_64 SDL2_image.i686 SDL2_image.x86_64 SDL2_mixer.i686 SDL2_mixer.x86_64 SFML.i686 SFML.x86_64

1.) Install all pre-requisites.
2.) Download the latest version of ModLoader64-GUI.
3.) Extract the contents of the .tar.gz file where you would like to install ModLoader64.
4.) Run ./modloader64-gui from the folder you extracted, this will populate the folders and perform a first run update.
5.) Download any mods and cores you want from the previous list.
6.) Copy paks files into their respective folders
Mods: ./ModLoader/mods/
Cores: ./ModLoader/cores/
7.) Copy rom files to ./ModLoader/roms/
8.) Congratulations, you have installed ModLoader64!

Arch and Derivatives

There is an unofficial AUR package listed here.

Video Settings

Found in the Emulation menu in the emulator window and require a full restart of ModLoader64 to take effect:

AspectRatio:
Stretch - Stretches to fit window.
Force 4:3 - Forces 4:3 regardless of window size.
Force 16:9 - Stretches image to 16:9 regardless of window size.
Adjust - Adjusts internal resolution to match window size.

Screen Width: Sets the default screen width of the window. (e.g. 1920)
Screen Height: Sets the default screen height of the window. (e.g. 1080)
FXAA: Enables and disabled fast approximate anti-aliasing.
Max Anisotropy0, 2, 4, 8, 16 Enables and disables anisotropic filtering at the selected multiple.
MultiSampling0, 2, 4, 8, 16 Enables and disables Multi-Sample Anti-Aliasing (MSAA) at the selected multiple.
AudioFast, Normal, Best Adjusts the audio settings to fit most common computers, changing this might fix stuttering.

The Legend of Zelda: Ocarina of Time Texture Packs
The Legend of Zelda: Majora's Mask Texture Packs
Super Mario 64 Texture Packs

Default Folder Windows (Rice) - %AppData%/mupen64plus/hires_texture/
Default Folder Windows (HTC/HTS) - %AppData%/mupen64plus/cache/
Default Folder Linux (Rice) - ~/.local/share/mupen64plus/hires_texture/
Default Folder Linux (HTC/HTS) - ~/.cache/share/mupen64plus/cache/
You can change the directories used for textures in mupen64plus.cfg

txPath = Path/To/Textures - Sets the path to Rice texture folders.
txCachePath = Path/To/Texture/Cache - Sets the path to HTC/HTS cache files.

It is recommended to set txCacheSize to 1000.

Settings

Rice Folder
txHiresEnable = True
txHiresFullAlphaChannel = True
GLideN64 .htc file
txHiresEnable = True
txHiresFullAlphaChannel = True
txEnhancedTextureFileStorage = False
txHiresTextureFileStorage = False
GLideN64 .hts file
txHiresEnable = True
txHiresFullAlphaChannel = True
txEnhancedTextureFileStorage = True
txHiresTextureFileStorage = True

Video Tutorial

ESC - Quit
F9 - Reset
Alt-Enter - Toggle Fullscreen
M - Toggle Mute
[ - Volume Down
] - Volume Up