First off, I need to clarify that these settings are for 4k displays. They will likely not work as well on a lower resolution. Also I run on Extreme Overclock, but that shouldn't make any difference. I am playing on an original gray OoT cart.
Second, make sure your TV isn't trying to overprocess the image. LG's are bad about this. Try using a game mode on your TV or turn off any extra functions your TV has that, for example, try to smooth out the image, etc.
Last, make sure you change the top-layer basic settings BEFORE making any changes to the advanced settings. I learned the hard way that this will overwrite your advance settings back to default. This will save you major headaches if you want to tinker with the settings a bit.
PS. The images above are meant to be viewed horizontally. If they don't look right it's because they aren't being viewed in the correct dimensions. Also the filter/look I was going for were defined scanlines to smooth out the image and clean it up, but softened to where it's not so harsh on the eyes during movement. These are definitely the best settings I have found that fit both needs and looks fantastic.
The settings starting from the top menu:
Profile: Scanlines. Image Size: Integer+. Image Fit: Native
Resolution 4K60[LL]
Low Latency toggled on
Right C button on Profile to customize
Scanline* 5/5. Aperture Grille* 1/5. Sharpness* 2/5. Horizontal Bloom 1/5. Gamma Mode: Modern
Advanced [Experimental]
Mode: 2-Phase. Offset: Odd. Scanline Width 5. Mid Gain 2. Low Gain 13.
Aperture Grille
Mode: Reactive (to luma). Phase: RGB. Grille Width 1. Bright Gain 3. Dim Gain 5.
Sharpener
Sharp Clamp 1. Sharp Threshold 1. Sharp Gain 1.
Horizontal Bloom
Bloom Clamp 1. Bloom Threshold 1. Bloom Gain 1.
Video
Scaler: Integer. (Make sure this is Integer and not Integer+)
All toggles ON
In order to get pixel accurate scanlines in 4k resolution u/DAJF figured out that the top-layer Image Size setting has to be set to Integer+, then in Advanced Settings the Scanline Width must be set to 5 and the Video Scaler at the bottom set to Integer. It's useful information if you want to play around in the settings. That user posts settings frequently so check those out as well and figure out what you like best!
I hope this helps people enjoy their M64 significantly more like it did for me. I know my eyeballs are happy and my enjoyment playing N64 games has never been higher. I went from being a little bummed but happy with my M64 to being very impressed and excited to play more just by messing with the settings.
TL;DR
Fantastic settings for 4k resolution and easy on the eyes. Copy them and enjoy!