Although I don't have all the medical names (if there are medical names), here are some other things that I've been reading about. IANAU (I am not a Urologist).
Poorly Done Circumcision - Without going into too much detail about the process, know that like any surgery, it is possible to make errors when performing circumcision, especially on newborns (as is the tradition in North America). From what I've read, the most impairing of these is with a circumcision is too tight, meaning too much of the penile tissue was removed which then causes the skin on the penis to be too taut when erect. This can cause a variety of problems, from erections simply being painful having the skin actually tear, especially along the coronal ridge.
Sensitive Skin - The skin on the penis, during intercourse, undergoes a lot of abuse. Most of the time it's pleasurable, however on a number of people, the skin in that area is hyper-sensitive to the point of pain. The friction of intercourse is too extreme.
There are also men who, for any number of reason, have pH sensitivities to the point where the pH of vagina will aggravate them. This is apparently common to those who have recently undergone chemotherapy or are using immunosupressants.
Testicular Cancer - Tom Green's disease, yes. In the more advanced stages of testicular cancer, due to your testicles destroying themselves, ejaculation can become very painful and will also occasionally be marked by blood on semen.
Prostate Cancer - A big deal in older men. The prostate can become inflamed, expands and constricts the urethra, and so when ejaculation occurs, semen is trapped behind the prostate and stretches the urethra.
Tissue Damage - Either through physical harm or by priapism, the erectile tissue of the penis can itself become damaged and even though the damage is not apparent during erection, the pain become evident when the penis undergoes compression during intercourse.