I was running a linux based system for 3 years and it worked great (jics.mp3car.com). Right now im re-designing the software (well, I'm writing a new one ;-) ).
I never concidered using windows for my car, mainly because of the tradeoffs and compromises you have to made if you use it.
Regarding the GPS navigation:
Personally I don't need a navigation system, but it is a sad fact that there is no usable linux solution available. The problem creating such a software is not the code, but the data. There is no vector data available in public. If the format of one of the big supplieres is cracked, the rest should not be a big problem.
The funny thing is,there's a navigation software for bikers under development...