I usually use emulation to dump videos from SNES and Genesis as well as edit my videos on Virtualdub2 (although I am looking into other software) but I had never edited videos from Nintendo 64, Sega Saturn or Playstation games before. Not all the games on those systems are 3D but I know that 3D games are different from 2D games. With that said however what would be a good way to edit the video dumps from Nintendo 64 and beyond games? I am currently using something called Bizhawk for the dumps.
I'm afraid we're gonna need a bit more info here. How are those recorded? I mean, which codec are you using to record, which chroma sampling etc? Also what do you mean by "editing"? If it's just trimming, it can be easily done in Avisynth, otherwise if it's something more complicated like a proper editing, I would suggest Davinci Resolve which is free, cross platform and pretty intuitive. (I personally use AVID Media Composer but the license ain't cheap). As to the upscaling part, from which resolution to which resolution would you like to go? I would suggest NNEDI3 but as I said we need to know more...
Avisynth so an AVS Script. I can send you a BAT to make your AVS Script encode in H.264 and AAC audio if you have never used it, but you're going to need to install Avisynth yourself and get plugins_JPSDR and ffms2