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The latest Gen III romhacking tools aren't really tools, but more decompiled source code and a text editor. Gen III has moved past binary hacking with a bunch of individual tools. Here is the link to the source code of the projects, and here is a link to a tutorial series on using them.
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SaaSHub
SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives
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Definitely recommend VBA-M
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Ironmon-Tracker
A Lua script for the Bizhawk/mGBA emulator compatible with Pokemon Fire Red, Leaf Green, Ruby, Sapphire, and Emerald that tracks relevant data for the IronMon challenge.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.
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Bi-Weekly Questions Thread
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[Gen 3] Using RNG manipulation and the Dewford Trend to Determine Feebas Tiles and Secret ID
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[pokeemerald] Figured out how to make running a toggle like newer games instead of having to hold B all the time
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PokeClassic: A Pokemon Yellow Remake in Pokemon Emerald.