I think..

Lucy's guild mark is Pink because of Natsu's hair color, and because of the first time she heard of Fairy Tail she saved herself and she saw her guild mark. (In memory days) Also it's a lighter version of red, which is Natsu's guild mark.

Natsu's guild mark is Red because of his magic; fire. (duh)

Erza's guild mark is Blue because of Jellal's hair. She missed him, and she lost him for what she thought would be forever, so it's sorta like a tribute to him.

Gray's guild mark is Dark Blue because... I honestly dunno. Maybe because of his hair...? Magic?

I think guild marks are also their favorite colors, and I don't think you really get to choose. The stamp is probably magic and chooses the color that best fits you, your personality, and past.