I'll first answer based on how I've been treated, which I believe wasn't too bad in term of thoroughness.
Steps include
- Visual inspection
- Palpation of penis and scrotum: more focused on scrotum at the start of puberty but moved on to the penis itself later. The only time the doctor touched my penis when I was 12 was to lift it up to facilitate an access to the scrotum.
- Retraction test: mind you, I was circumcised, but inspecting my penis while flaccid might have required this, for it to go all the way back.
- Tanner staging: no orchidometer or measurement, just assessment after the first step
- Erection Response Test (only 1 time at eighteen): a few strokes but done by the doctor, not really erected but my member did react.
But here are what I think SHOULD be done to all males, especially from puberty onwards --> pre-employment exams
- The steps above consistently.
- Penile measurement (length and girth, flaccid and erect) to end those male insecurities. Let the doctors solve this problem once and for all.
- Semen collection to ensure fertility.