Maybe you should just fix the real problem? It sounds like you are trying to compensate for bad hardware. Wrongly I might suspect. You don't want to change the pitch, you want to apply an equalizer effect to compensate for the poor speakers.
To be clear, this is incorrect -- it's not
an EQ issue, and the OP asked for exactly what he wanted, as AtGames units definitely play the music at the wrong pitch.
From what I've heard via YouTube captures, they're about a major third too low, so that'd be a 4/5 ratio, or 20% below the correct frequencies. Here are two videos from Sonic to compare:AtGames unitCorrect versionThis video review
also has multiple examples, with Sonic featured around 12:30. The title screen music is in F, vs. the original A; the Green Hill Zone music is playing back in A-flat, vs. the original's C; and so on. At least in the case of Sonic, it seems pretty consistent, and the music in the Mortal Kombat clip at 20:00 is also 20% too low.
As for how to fix it, I have no idea, and outside of the usefulness of knowing how Genesis games handle their frequency tables, it'd be wasted effort to "fix" games for a bad clone like AtGames's effort. I suppose you could always send the audio through a real-time pitch shifter!