The wireless GH3 Les Paul and the GHWT Genericaster seem to have the best compatibility since they are oldest. Both work with every music game with the sole exception of Rock Band 1 and early RB track packs. Unfortunately, both has some hardware issues - GH3 guitars are prone to poor fret response after the neck comes loose over time, and GHWT guitars have unreliable strum bars. Also, neither can use many of the Rock Band-only features (FX switch, solo tap buttons).
I use two GH3 Les Pauls, one GHWT guitar, and one RB2 strat.