My car stereo has an aux send/return, I use Stereo Tool on a laptop instead of the built in EQ. Mostly I use the pre-amp, bandpass filter (12Hz-22kHz), subtle noise removal, AGC, subtle multiband compressor, and the single band compressor. For this, I don't generally use bass boost, stereo imager, loudness, the final limiter, or the input declipper (which is AWESOME btw). I have had very good results lately also using the new bass AGC along with some mild bass clipping in the multiband compressor, to reduce bass spikes coming out of the AGC.
I use it to tune the output to my speakers, and to improve volume and EQ consistency between songs.
This is a pipe dream, but a touch-screen optimized interface would make this really fun. Then I could run it on one of those in-dash touch displays, e.g.
http://www.xenarc.com/product/MDT-X7000.html.