Provide full game titles from the CRC or title. Store cheat codes to let you cheat in a game. There are limitations. You can only turn on and off features that already exist in the emulator. You can't perform miracles.
Most problems require a new release of the emulator to fix.
If you read the emulation news sites you'll often see that half their stories are INI releases. This is because there are loads of people involved in writing the INIs, some of them on the official teams, but most produced unofficially. There is often no coordination between authors. As a result of all this, it is not uncommon for later releases to be missing games that another author included ages ago. As a rough rule though, the newer unofficial INIs are best.