I bought Rock Band (which is on sale at Target this week for $157, btw) tonight. I spent the last hour playing it on my PC with Frets on Fire, and I can happily report that the PS3 Rock Band guitar works with Frets on Fire just fine. The wireless dongle shows up as a USB HID device in Windows XP, and it shows up as a normal game controller. You can then map the guitar keys to the appropriate controls in Frets on Fire.
So why is this related to anime? Well, much like Stepmania, there's a whole community of people that make files for Frets on Fire, and you can find things like God Knows for it!
And supposedly the Rock Band drums work with DTXMania, though I haven't tried it yet. And yes, there is God Knows for the drums as well, though I haven't tried it yet (too lazy to unpack the drums tonight).