Most of the roms are fairly well understood from a reverse engineering perspective; especially gen 1 (red/blue). That's how bugs that were known back in the day but people weren't sure /how/ (note how some like the item duplication bug or the Mew bug were sometimes called 'cheats') are now fully explainable (usually as memory management bugs).
...which eventually leads to figuring out how to write arbitrary values to RAM and jump the CPU to execute those values. Witness the Pokemon Yellow Total Control Hack:
They've also reverse-engineered the RNG. You can capture a high-level Pokemon, and then brute-force the RNG on a common desktop PC faster than the game can generate it, so you will have a high chance of getting some rare thing to happen, provided you can hit the button within the proper tenth-of-a-second. I looked at writing this but got busy with other things.
Generation 4/5 also had a number of other ways to manipulate another RNG, that basically made capturing high-IV and shiny Pokemons almost trivial. People wrote Windows desktop applications to tell you exactly how many times to flip a coin to get the RNG exactly where you wanted it.
There's a big debate in the Pokecommunity whether or not this is cheating. You can probably figure out both sides big arguments already.
>Generation 4/5 also had a number of other ways to manipulate another RNG, that basically made capturing high-IV and shiny Pokemons almost trivial. People wrote Windows desktop applications to tell you exactly how many times to flip a coin to get the RNG exactly where you wanted it.
Great, you probably just got me playing again. There goes my free time ;)
Pretty cool nonetheless.