Only use the colors marked as "Normal". All other colors are action colors and might appear flashy or otherwise different ingame than in your sprites.
Excaptions are the Transaperent blue which you need to put around your sprites in a box shape, so you won't get white areas around your sprites ingame. More of this explained in the tutorials.
Then there's the "Company" colors. Some sets use this, so they player can choose the vehicle's color ingame, like the original vehicles.
A patch has been made for a second company color. This color can be used for a second company color for the player to choose, or for a real color. In the GRF it's specified which of the two options is chosen.
www.ttdpatch.de has a page with extended information on the palette.