If your semen has a red or brown appearance, it is probably from a burst blood vessel in the prostate. This can happen with normal ejaculation, and within a day or two, the semen should return to its normal color. If the discoloration continues for longer than a few days, you should see your doctor. Persistent blood in the semen may result from infection, trauma, and rarely, cancer.
Normal semen may have an off-white or slightly yellow tint. Semen with a pronounced yellow or green color may indicate an infection, possibly due to a sexually transmitted disease called gonorrhea. Go to your local STD clinic. If your semen is discolored due to a gonorrhea infection, treatment with antibiotics is necessary.
Foul smelling semen is nearly always a sign of infection. Go and see your doctor.
Sources: http://www.netdoctor.co.uk/menshealth/facts/semenandsperm.htm http://www.mayoclinic.com/health/discolored-semen/an00779