If your semen is stained with a red or brown colored fluid it may be caused by blood. Sometimes a small blood vessel may burst when you ejaculate. Within a day or two the semen should return to its normal state, so there should be no need to worry. If it continues then you should see your doctor. Blood in semen may be present for many different reasons, such as infection, trauma and sometimes, but rarely, cancer.
Normal semen may have an off-white or yellow hint to the color. Where semen is uncharacteristically yellow or greenish in color it is a sign of infection, often due to a sexually transmitted disease called gonorrhea. Go to your local STD clinic. If it is gohorrhea, treatment is simple with the use of antibiotics.
Foul smelling semen is nearly always a sign of infection. Go and see your doctor.