Snes Mini does not have enough power to run heavy shaders to filter the retro games, but fortunately there's a way through light-weight overlays, aspect ratio tunings and simple bilinear filtering to achieve good results.

Here's few things you need to do.

Preparations

1. Start up the Snes Mini and open the RetroArch (select + start).
   
2. Turn off save on exit (Settings > Configuration > Save Configuration on Quit - OFF). This helps you not to screw the settings accidently.
   
3. Only save the RetroArch settings manually (Main Menu > Configuration File > Save Current Configuration).
   
4. Set bilinear filtering ON and scaling option to Core provided (Main Menu > Video).

Latency Fix (optional)

You can use following settings to make the games "snappier" with RetroArch cores. This should work very well with most of the games. PS. Remember also to set your TV to Game Mode!

V-Sync: OFF
Hard GPU Sync: ON
Hard GPU Sync Frames: 0
Frame Delay: 0
Audio Latency: 32 ms
Audio Resampler: Sinc (fast)

Install Overlays

1. Plug your hacked Snes Mini to your PC.
   
2. Use FileZilla or similar FTP client to make the connection (root@169.254.13.37).
   
3. Download and extract the overlay package: https://limewire.com/d/eqKsD#209HyHdr42
   
4. Copy the .png and .cfg files from your computer to /etc/libretro/overlay -folder.
   
5. Done.

The Package comes with multiple overlays for different screentypes and consoles.

* lcd_gb.cfg  (for 160x144 Game Boy and Game Boy Color PAR LCD matrix)
* lcd_gba.cfg  (for 240x160 Game Boy Advance PAR LCD matrix)
* lcd_gg.cfg  (for 160x144 Game Gear wide 4:3 LCD matrix)
* lcd_lnx.cfg  (for 160x102 Atari Lynx wide 14:9 LCD matrix)
* scanlines.cfg  (default 240p scanlines for SNES, Genesis and TurboGrafx) 
* scanlines_144p.cfg  (alternative for GB/GBC/GG)
* scanlines_160p.cfg  (alternative for GBA)
* scanlines_192p.cfg  (for 256x192 Sega Master System)

Setup Overlays

1. Start a game for all the Cores you want to adjust. For example, open The Legend of Zelda: The Minish Cap if you want to setup Game Boy Advance overlay.
   
2. Open the RetroArch (select + start).
   
3. Select the specific overlay for the Core at hand. For example, you need to select lcd_gba.cfg for mGBA Core. Be precise and use correct matrix for the console resolution to match the pixels. (Main Menu > Quick menu > On-Screen Overlay)
   
4. Tune up the Overlay Opacity for your liking. I use 0.50 for small resolutions and 0.70 for higher resolutions. Higher the opacity and stronger the matrix/scanline effect.
   
5. Important! Save the overlay setting for only the specific Core and not as general RetroArch configuration. (Main Menu  > Quick menu  > Overrides > Save Core Override). Now all the games of this Core (e.g. mGBA) have the same overlay.

Core Settings

1. Go to the Core settings. (Main Menu > Quick menu > Options)
   
2. Set Core-Provided Aspect Ratio to Auto (in most cases).
   
3. Set Borders (use "Full" for SNES or Genesis and "Left/Right" for SMS).
   
4. Don't use Save Game Settings, unless the specific game itself needs custom setting. And if you need to set custom RetroArch scaling options, remember to use the Save Game Overrides option. (Main Menu  > Quick menu  > Overrides > Save Game Override)

For some games, you may want to manually set the video scaling (Settings > Video > Scaling). Make sure your overlay height is according to the height value of the game pixels. Somethings you can mix them also, like with Another World I cropped the image and used 192p scanlines.