My personal favourite is to keep within the same umbrella of manufacturers; A Mini using a BMW colour, or a Prowler being painted Plum Crazy, things like that.
I also tend to do that although I don't strictly limit it to the same manufacturer but broaden the scope by links between manufacturers.
Given the incestious, or opportunists, nature of the car industry that obviously means almost all car brands are in some way linked through past and present collaborations or connections ofcourse but some combinations seem more 'appropriate' than others.
For example my
Grigio Ferro Fiat 500 (the new one) is rather obvious, my 2 Paganis Zonda R painted in Mercedes-Benz colours slightly less perhaps and there are other less obvious combinations.
There are exceptions, Lotus being the independant engineering consultant (often secret) for a lot of different brands is the perfect 'excuse' to paint a lot of different cars in my garage in a Lotus colour (although that has more to do with me liking a lot of Lotus paints like
Gunmetal 
).
And if I just like a certain colour on a certain car which aren't linked I can be equally opportunistic as the car industry.

Recently I've read an article about the Miura and it showed pictures of one in a colour called Oro Metallizzato which I wanted on one of my Miuras, the only colour I could find in GT5 which came close (and had a nice sounding and similar name) was
Oro Chiaro coming from a Ferrari 512BB.....so I cheekily painted it that.
Or maybe I'm just taking this videogame a bit too seriously....