To install a mod, simply extract the .zip folder into your Braid installation directory
This is usually C:\Program Files (x86)\Steam\steamapps\common\Braid if you bought the game from Steam
or C:\Program Files (x86)\Braid if you bought it from elsewhere, though the path can vary (mine is neither of those)
To run a mod you have installed, run Braid with the -universe <folder name> launch option.
If you are using Steam, you can most easily do this by right-clicking Braid in your Steam library, opening the preferences and selecting launch options.
In all other platforms, you can simply run the executable directly with that option, either with a shortcut or the command line.
A mod launcher will be created eventually, though there is no specific timeline on its creation.
After the Epilogue, After After the Epilogue, Mora Now Than Ever, Silverbraid, and Secrets mods hosted with permission from the creators.