I'm dragging this post back from the dead because I finally got a 2006 Prius and intend to stick my empeg in it. As I do, I'll try to document things a little bit for posterity just in case anyone else is looking to do this in the future. It'll also be a good reference for me to go back to and remember what I did.

I'm going to start by summarizing the current state of Prius/empeg connection options. All of the information in the previous replies is still pretty much valid, but there are some easier options now.

Coastaletech has still not come up with a good audio hookup option for this generation 2 Prius. He's showed some prototypes of a full AV interface as well as an iPod interface, but none of that's come to pass. Even if they were available, he's a sketchy source. The dude has zero business sense and thinks nothing of sitting on an order for a few months without any sort of communication until more parts become available.

There are several devices that'll hook up to the CD changer port on this gen 2 Prius and provide aux input. Some of them will allow an additional CD changer to be hooked up, some will replace any possible CD changer. Some of them also have full iPod integration or satellite radio hookup or things like that. Using one of these things would make the actual audio wiring much easier. I don't have any idea which one of these might work better than any other, but if I look into it more, I'll post findings here.

Additionally, the 2006 models (except package 1, aka the fleet/rental car package) have a 1/8" aux input jack in the center console. This jack also presumably has a switch that signals the stereo that something's plugged in. The stereo only makes the aux input available for selection if something's plugged in to the jack.

Some packages of the gen 2 Prius have Bluetooth phone integration. When making or receiving a call, the audio mutes, and the CD player actually pauses. I do not know if this is exposed in a mute sense line anywhere or just dealt with over the CAN bus, but I intend to find out and hopefully use it.

Mounting is still the same. The compartment under the stereo is still the best place to mount it, and I doubt anything physical has changed behind the dash that would make mounting more or less difficult. It's still going to require removal of the compartment and a little trimming, and will still look excellent when covered by the door. The only possible change is there might be a tiny bit more room behind the dash above the compartment, since the cassette player has been deleted from all configurations. However, I suspect the size of the factory radio's enclosure is still the same.

So, it appears I have a few options. Power and ground would be connected the same way for all of them. The possible hookup of a mute line would be the same for all of them. The volume would all be controlled by the car (so I could still use the steering wheel for that). The audio would just take different paths.

Option 1: Brute force the wires into the signal path like Neutrino did. Basically tap into the audio path going from the head unit to the amp and use a relay energized by the empeg's amp remote wire to switch the audio signal. To the best of my knowledge, this would still work. I have the JBL system, which I believe still has an external amp for 2006, although I've read differing things on the location of the amp (in dash vs. under the driver's seat). And, I'm assuming that electrically, the signal from the head unit to the amp is the same (although the wiring colors my be different). If one had the non-JBL system, it might not have an external amp, and if not, you'd have no path to tie into there. Pros: cheap, doesn't mess with or tie up any of the rest of the system. Cons: a bit of a complicated install. Plus, you can easily get into a situation where audio's coming from the empeg, but the CD transport is still spinning, losing your place when you come back to the CD. A possible solution to that would be to somehow tie the empeg amp remote wire to the hypothetical mute sense line in the car to pause the CD when the empeg switches on.

Option 2: Use some sort of auxiliary adapter to get the audio into the stereo. This lets me just pick the empeg as another source on the head unit. Pros: dead simple installation, as most of these things just take RCA style inputs right into them, and then plug into an empty port on the back of the head unit. Gives me all sorts of other possible options, like integration of satellite radio or ipod with the touch screen. Cons: They can be expensive; $200 or more for the fanciest. Also picking the right one can be hard. If I want iPod integration, which one does it best? Will they all handle the 4v outputs of the empeg? Are any of them more prone to ground loop noise than any others? Also, it's easy to switch sources away from the empeg and leave the empeg running, which would lose your place on the empeg when you come back to it. If there were such an aux-in device that somehow gave some electrical indication that the aux source was currently selected, I suppose you could tie that into the empeg mute line to start and stop it. I wonder if there's any wire that goes between the head unit and the aux-in box that's only powered when aux-in is selected? If so, that could tie into the empeg mute line and start and stop it. I don't know if that would keep me from tying in the hypothetical Bluetooth mute line, though.

Option 3: Use the existing aux-in signal path on the 2006. The cheapest and easiest way might be to just run a cable up to the center console and plug into the aux-in jack. Aesthetically, that's goofy, though. So, what I'd probably do here is just tap into the aux wires before they get into the head unit. I would need to then somehow trick the head unit into thinking there's something plugged into the jack. I'm guessing I'd accomplish that by tying the empeg amp remote wire to the wire coming from the switch part of the jack, or using the empeg remote wire to trip a relay closing the switch circuit or something. That way, whenever the empeg was on, the head unit would see aux as a valid source selection. I don't think I'd need a relay to switch the empeg audio in an out of the signal path, though. From what I'm guessing, this would be the equivalent of using a Y adapter to put two audio signals into the same input. Now, when I want to plug something into the existing aux-in jack, I can do a couple of things. I can just turn the empeg off and let only the other aux-in signal come through. Or, I can actually have the switch in the jack fire a relay that switches the empeg audio out of the path and even mute or cut power to the empeg. Or, I can wire the existing jack solely to the empeg's aux in, and use its switch to signal the empeg to go to aux in mode (although that would keep me from using the mute line for phone mute purposes). That would require the empeg in car to use the aux in, though. Pros of this option: Can be a pretty capable semi-automated installation with a lot of flexibility. Can be pretty easy if I don't go overboard. Cons: Could get ridiculously complicated very quickly. Could still change sources and lose your place on the empeg. There are existing ground loop problems when using the aux input with a device that's powered from the lighter port. That my portend the need for some sort of ground loop isolator in this kind of installation.

Other notes: Oh how I wish for a way to control the empeg from the Prius. I would be so happy just to have the track buttons on the steering wheel send forward and back commands to the Prius. I have very rudimentary electrical skills, and certainly no CAN hacking skills, so I can't make this happen, but how I wish someone could.