I've been playing X-Wing vs Tie Fighter lately, and I love the different squadron markings on the various fighters. I've begun painting marking stripes onto my TIE Fighters to see how they look -- if it doesn't work out, it's easy to fix. I've chosen two thin orange stripes, horizontal, near the top and bottom of each solar array. I may do the same to my Interceptors when I get some.

I'm planning to do my rebels in green.

Anyone else go with a different colour scheme? I'd stick with black TIEs and red X-Wings, but I'm something of a hipster -- I've got to be different.

When I get the stripes done I'll upload pictures.

 You can always paint a green squad and a blue squad for your X-Wings.   Originally, the X-Wing squad that attacked the first Death Star was supposed be blue, but as they were using blue screens for soecial effects, it messed with the effects so they repainted them red.  

Also, Y-Wings can be repainted gray.   The different color squads will make it unique and will be pretty cool.  

I figure that the films show some markings being different so there must have been a variety of markings and colours used. We don't see much on TIE Fighters, but the 181st in the EU have red stripes.

I don't see any reason not to use green on X-Wings, blue on Y-Wings, or yellow on A-Wings, or any primary colour or shade. Black might actually look pretty spiffy on A-Wings. After all, there's so much left unexplored and unwritten in the Star Wars universe, so who's to say such markings weren't used?