As mentioned above, sperm are made in the testes. During sexual intercourse, smooth muscles contract and propel mature sperm from the end portions of the epididymis through a long tube (vas deferens or ductus deferens) inside the body, just beneath the bladder. From there, the sperm get mixed with nutrient-rich fluids from the seminal vesicles and a milky secretion from the prostate gland. This combination of sperm and fluids is called semen. The semen does three things: 
Provides a watery environment in which the sperm cells can swim while outside the body 
Provides nutrients for the sperm cells (fructose, amino acids, vitamin C) 
Protects the sperm cells by neutralizing acids in the female's sexual tract 
Once the semen is made, it passes through another tube (urethra) within the penis, exiting the body through the opening of the penis. 

One last male organ is a tiny, pea-sized set of glands inside the body at the base of the penis, called the bulbourethral or Cowper's glands. During sexual excitation, and just prior to the ejection of sperm (ejaculation), the Cowper's glands secrete a tiny amount of fluid that neutralizes any traces of acidic urine that may be leftover in the urethra. It is also believed that these secretions are designed to lubricate the penis and female tract during sexual intercourse.