Generally you're screwed if you're a RB/GH fan and only own the PS3. The GH3 guitar will only work with GH3 and not previous PS2 versions of GH. I've read that you can buy a ps2/ps3 adapter but the PS2 guitars still don't work right for playing the older games.
If you own an xbox 360, the guitars work on both games (RB/GH) and you could buy/download all the GH content (except for the 80s game) and play both games while only cluttering your house up with one guitar. It sucks and you can blame activision for being pricks about it.
There was talk of a 3rd party guitar (I wanna say Nyko Frontman, but I could be wrong) being able to work for all GH/RB games on the PS3 but it wasn't confirmed last I heard.