Shopping for the thing is easy as there isn't any haggling, so the big decisions are. A "Yahoo":http://autos.yahoo.com/newcars/scion_xb_2006/4537/model_user_reviews.html;_ylt=Al1IHSuUY81qXco1zVyVYAM8l8AF?sort=mh&modelid=4537&start=1&show=atf&reviewid=7&reviewnum=1&trimid=17751 review points out that most of the OEM accessories are available on eBay, so if you want these, the cheapest way is to find a local tuner in town or to buy on eBay and install yourself.
The 2006 model adds a standard audio jack so the audio input goes in easily. For an additional $260 bucks, the stereo itself can show the song playing on the iPod. Personally, the $260 doesn't seem quite worth it, because for me, the iPod itself is a nice enough user interface.
Alarm system. $400 for this, seems like a good idea to get an integrated one, although "Car Toys":http://cartoys.com can outfit you after market. I had an after market system for my original BMW and I kind of like the integrated ones better, but don't know if things are better now.
Leather seats. OK, the thing doesn't come with leather, you have to change that after market and it is expensive. So cloth ain't so bad now that the kids are older.
DVD Navigation System Eclipse ESN E5. Again, these are after market, "Scionzone":http://forums.scionzone.com/yabbse/index.php?board=3;action=display;threadid=500 recommends an Eclipse unit that fits into the standard double DIN radio slot. The "ESN E5":http://www.eclipse-web.com/avn/avn5435.html has a DVD navigation, MP3 playing. You can watch a DVD, but only when the car is stationary (how depressing!). Both Car Toys and Magnolia Hi Fi carry it. It is incredibly easy to install an aftermarket radio according to this post.
* remove the three climate control knobs, yes the just pull off.
* then remove the philips screws under the two outer knobs locations.
* then you will have to gently pull the bottom out on both sides. pulling in a downward but outward motion, this will allow the top to swing out and unclip.
* gently disconnect the heater controls, Hazards and additional plugs on the back of the bezel. Place this in the rear to keep from scratching the unit.
* next remove the 4 philips screws and detach the power plug on the rear along with the antenna.
* at this point you should have a gapping hole in the dash and a smile on your face.
Performance-wise, there are some things to get and there is an incredibly techie post on "ScionZone":http://forums.scionzone.com/yabbse/index.php?board=3;action=display;threadid=245 that I'm still trying to decypher. The important ones are:
* Manual "Transmission":http://www.scionlife.com/forums/viewtopic.php?t=85493. Manual is definitely peppier, but there is a two month wait for them 🙁
* Air "intake":http://forums.scionzone.com/yabbse/index.php?board=3;action=display;threadid=27. These parts "open up" the air input, so you get better performance. AEM Cold Air Induction is what Scion sells, but they also recommend the Injen version. They also hurt gas mileage. Not hard to install, but if you are noob, then let the dealer do it.
* Exhaust Manifold. Strup makes one that is good, the DC Sports Header costs more but is also good.
* Exhaust system. To really get best performance, you have to put a full catback in. Sounds expensive.
For the suspension and ride performance, again "Scionlife":http://www.scionlife.com/forums/viewtopic.php?t=65648 has a bunch of recommendations:
* Rear Shocks. The front shocks are fine, but the stock rear ones are harsh. Change the rear shocks to Koni 80-2827 Sport (this is the model for the Toyota Echo, which is mechanically a Scion xB) and things get better for just $196 at "LTB Motor Sports":http://ltbmotorsports.com. You can apparently do this yourself in 20 minutes just with the right tools. Tirerack.com also carries them.