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If I were doing this myself, this universal 'Toyota ViewTech 2005 Controller' solution looks best to me from the perspective of plugging in 'Whatever', including other aftermarket navigation, computer, video, etc. widgets. I'd mount the little yellow box somewhere that I could get at it behind the dashboard, probably with double-sided sticky tape. It integrates switching audio/video into the Prius buttons for two channels of video/audio inputs, and doesn't get in the way of XM or other stuff.
http://www.coastaletech.com/viewtech_2005.htm
At $300 it's a bit pricey, and it looks like there's a backorder of 6~8 weeks, but you're the one who bought a prius....
Possibly a car profile DVD/MP3 player could be plugged in, so you could get the track information displayed on the Prius screen, but you'd have to shop for that 'perfect' device. Later on (assuming you don't kill yourself watching movies while you drive), you might add an aftermarket satelite navigation system using the extra set of inputs that are already conveniently there.
I would set it up on 'SAT 3' (per the description on the web site), so the MP3 screen could be shut off without shutting off the audio, but that's just me. I can't stand junk animating at me from the dashboard.
This other web site has FAQs and technical information about another different plugin (which only works on the earlier Prius models, as it turns out), and an illustrated guide, which (even if you don't use this solution) does give you an idea of what's mechanically involved in plugging in an aftermarket radio.
http://mywebpages.comcast.net/bumpelo/index2.html
http://mywebpages.comcast.net/bumpelo/install.html
Apparently, the second device treats the MP3 player like the toyota six disc 'CD Changer', and provides on-screen Prius navigation for it. Of course, the Jensen players he provides with the adapter are panned in reviews pretty universally, so I'd be looking for the adapter without the radio, and shop for a better Jensen radio that still uses the same IR codes. 'Jensen' is key here because the gadget sends commands to the IR remote receiver on the Jensen. Nothing on the site about programming the same microcontroller with other car radios' IR codes, though that should be theoretically possible, given an SDK for the microcontroller in use. Of course, if the CD navigation from the Prius screens is a secondary concern, I bet this would work fine with any radio, it just won't tell the player what to do from the Prius touch-screen.
Someone said they successfully installed this radio thing, but they might be a shill...
http://priusonline.com/viewtopic.php?t=23
Of course, I have a Honda and am content using a $130 JVC MP3 stereo with my stock speakers. I am not an 'audiophile', in that I can't tell the difference between a $200/foot monster cable and a lamp power cord bought off a spool at the hardware store when connecting speakers. I certainly can't tell the difference with wind, road noise, traffic, etc. while I'm driving between a $130 and a $500 radio. That's just me.
I'm just a USAF trained electronic/computer technician who has been programming computer software and computer games for a living for the past 15 years, and maybe understands a thing or two about electronics and interfacing computers to things as a result.