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 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 activates 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."