I was around during most of the reverse-engineering efforts, as I'm the original author of
nestech.txt. So if you're wanting a history lesson, I'm probably one of several people to ask. I gave an in-person interview several years ago with JoeGtake2 for his documentary
The New 8-Bit Heroes but the footage was never used (several other nesdev folks are in it).
I recently got asked
similar questions about the early snesdev days, wherein I did briefly touch on NES/nesdev stuff (if you read my posts/answers, it'll become clear why I do that). The earliest forms of RE, i.e. "pre-emulation" days, were being done by two select people in Russia (Alex Krasivsky (wrote some code in iNES, and also did his own emulator, LandyNES) and Marat Fayzullin (iNES emulator author, author of NES file format); I'm still friends with Alex to this day) on the Dendy. This was a combination of hardware analysis (esp. to dump carts to ROMs), and software RE. There was were also some efforts going on in Asia (Japan/Taiwan/HK) but language barriers and general cultural/societal differences (what chat networks were used, etc.) didn't make sharing of information there possible. Later information happened as a result of the emulation boom in 1996 onward, which is revolutionised understanding the console's more intricate aspects (particularly the PPU); loopy's
skinny.txt was one of those aspects. Emulation in general is what really spurred a substantial amount of the knowledge we have today, and most of that was time spent by people doing emulators who sat staring at disassemblies of commercial games. But the very intricate and complicated details of behaviour required hardware-oriented folks (read: people with EE backgrounds), so nuances and explanations for "why that thing has to be done that way" became known once more hardware folks got involved. Otherwise I'd suggest buying
Nathan Altice's book titled "I Am Error" as it's a wonderful read and gives insight into lots of things.
It's true that Nintendo's patents were (partially) reviewed for some RE aspects that lead to discoveries on the NES, but IIRC, the only useful thing found in them pertained to one of their mapper patents (no I don't remember which one; possibly MMC2?) and that piece of information acted as confirmation of something/behaviour already known. I don't believe there wasn't anything "console-specific" that was found to be useful in patents. Technical patents these days that surround IP are *intentionally* written this way (I like to describe them as "specifically vague/nebulous"), and USPTO has a very bad habit of approving them.
I'm glad there's a compiled list, though. The links probably don't work because of USPTO website link changes, or possibly an account is required; not sure. I'm certain someone could go through and verify + fix them all.