Pre-requisites:

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

1.) Download the latest installer or zip.  The installer includes prerequisites, the zip is for manual installation.
2.) Run the installer or manually extract the zip file. If using the installer, skip to step 6.
3.) Run modloader64-gui.exe to run the first time update and to populate folders.
4.) Download OotOnline.pak (Mod)SuperMario64.pak (Core)Sm64Online.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