For those of you who have a stock stereo and want to upgrade, I can highly recommend these two I just helped to install to my friends:
JVC KD-AVX1 – has small built-in screen, connected it to rearview camera on my friend’s 4runner; also can play MP3s from DVD-R, so you can record 4GB worth of music and just put it in your dash. Has optional AUX input to connect iPod, but why would you need it with 4GB disk?

great sound! Installed it with Polk Audio speakers and DIY subwoofer.
Pioneer DEH-P9600MP – plays MP3s from CD (not DVD), plays DVDs, has compatible with Pioneer's iPod interface adapter – you control iPod like it’s a CD changer, using stereo controls; lots of adjustments and customizations, absolutely greatest sound I’ve heard so far after I adjusted all the parameters. Installed it on friend’s Audi with Focal speakers (had to rip off stupid Bose system), now he’s in sound heaven.
Pioneer AVIC-D1 – navigation, rear camera view (no DVD playback). The rest is same as for DEH-P9600MP. Installation is not easy, don’t DIY unless you know what you’re doing. Installed it with Pioneer GEX-P10XMT XM NavTraffic Satellite Radio, it gives you real-time info on traffic, neat!