Rock band instrument compatibility

Currently:

What we know:

• Most, if not all, of the legacy catalogue of RB(meaning all the DLC along with the past games) has been charted with the cymbals one uses with the pro drums. If you look at the animations of the drummer in-game, you'll notice that the drummer will play on the cymbals or on the toms on notes of the same color. This is not conjecture based off of that, however; HMX reps confirmed this.
• Everything new with the keyboard and guitar controllers will only be available for RB3 and all forthcoming DLC(from RB3). Same source.
• "There are a lot of cues and “hooks” in [HMX's] authoring flow that have always been there; [they] just haven’t had the software cycles to take advantage of them". Again, same source.
• Harmonix will be re-releasing some old DLC with full support for RB3's new features. Currently they are asking for the community to chime in on which songs they would like to see re-released first.

What we don't know:

• What exactly the cues and "hooks" are aside from the drums. I have, however, noticed in-game that there are times in RB2 when the guitarist and the lead singer will sing together, implying that some of the songs in their legacy catalogue may have support for vocal harmonies in RB3. No concrete evidence, though.

Updated August 16th: HMX will be re-releasing old DLC with full support.

No, only the Squier (and other MIDI-guitars) will work.

From Game Informer, Issue 209 (pg 32):

"Due to technology in the neck the Squier does not need to be re-tuned to alternate tunings," Baker assures us. "No capos are needed to play the game." ... Baker says you don't need to be in tune to play the game.

...

"The Rock Band 3 Squier Stratocaster uses technology built into the neck and fingerboard of the guitar to track finger positions in real time," explains Baker. As a player holds down a particular fret and string, the onscreen display will show that note and string, giving players feedback on correct finger placement even before the note is picked.

What all this means is the game tracks where your fingers are and when you pluck, not the sound the guitar makes.

It's theoretically possible that an accessory could be made to play the game using only the sounds made by a guitar, but doing this is notoriously difficult (and impossible in truly real-time - see this page and @Jeffrey's comment below), and would likely be very inaccurate and frustrating.

I've looked all over for the converter mentioned by @jblaske in the comments above, but can't find anything. He is probably thinking of the Rock Band 3 MIDI Pro Adapter, used to play Rock Band 3 with midi-keyboards and midi-guitars (not the same as electric guitars!).