To crop out borders, use MeGui's AVS Script Creator.
Give MeGui the video file, select crop, and start cropping. You can use Auto-Crop, but it is not always perfect (sometimes will eat more than needed). Just adjust accordingly. Then go to the script(? Can't remember. Not on XP. It is one of the taps) and copy and paste the crop script
After cropping, maybe resize the video to a system's native resolution (for SNES, it will be 256x224)
You can also crop out black borders using virtual dub. Just go edit -->Filters-->click on null transformation-->click on crop selection and then press up or down for X1, Y1, X2, and Y2 to crop out black borders. That's it.
And then you will have to save a new video file and wait for that to finish.
Why do that when you can just use AviSynth to crop (again, use MeGui's AVS script creator to find crop values. Auto Crop is really useful, but if it chews off more than needed, it can be adjusted.) and encode the files like you normally do with MeGui (y'know...make Mp4 files and then mux).
That is what I did when I did Parasite Eve: cropped the void from RemoteJoyLite, did some stuff, made MP4 files. Didn't have to use VirtualDub to make a new video file (I only use VirtualDub to find the frames and "trim" them out.)
Virtual Dub is used a lot for editing. If you have to edit your video in Virtual Dub before encoding you might as well crop out black borders in virtual dub. That way you won't have to worry about it in Megui. There's no wrong way which to use to remove black borders. Either Virtual Dub or Megui should work. I see JonL's idea of removing unwanted frames in Megui, is more complicated to do it that way. It's much easier to to remove them manually in virtual dub especially if you used 1000 save states in emulators that does not have ReRecording.
SchLauchi recommends to edit your videos in virtual dub if it needs editing before encoding in Megui. I submitted longplays since last year and always done it that way.
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