According to early tests conducted by IGN, the most compatible controller is Xbox 360's Guitar Hero 2 X-plorer model, which works with both upcoming titles, although you cannot use the special effects due to the lack of a five-way switch. The GH3 Les Paul controller works with everything except the PS2 version of GH2 (played on a PS3, natch) and, like the X-plorer, cannot activate effects.
Rock Band's Stratocaster, however, does not work with any Guitar Hero title on the Xbox 360. (IGN has not been able to test the PS3 version yet.) A statement released by Harmonix said, among other things, that they "welcome any 3rd party software that wishes to support Rock Band guitars. If a 3rd party guitar / music game does not support the Rock Band guitar controller, questions regarding this should be directed to the game manufacturer." There is no word yet from Guitar Hero publisher Activision. And when everything is finalized, we'll be sure to make you an colorful, easy-to-read compatibility chart.