These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Subverted with amputees; as Bud Roberts gets a leg amputated as result of stepping on a land mine in Afghanistan, yet he's ultimately able to fully recover (with the aid of a prosthetic leg) and to live a happy familiy life.
Averted with homeless military veterans who are portrayed as sympathetic people who need help to re-enter society.
Acceptable Professional Targets: The show, being about lawyers, does employ a few obligatory lawyer jokes. Within the military setting itself, the show also demonstrates that this trops is true within the American armed forces, with servicemembers of various occupations or branches making jokes at each others' expense (Marine infantry vs lawyers, Naval aviators vs. everybody else, commissioned officers vs non-commissioned officers and enlisted, Navy vs Marines, etc.)
Acceptable Religious Targets: Fanatic and outright anti-American Muslims with hostile intentions were always legitimate villians on this show. However, Muslims who does not express an open anti-American sentiment are portrayed quite favorably.
Actor Shipping: There was/is a lot of shipping among fans, often in the form of fanfiction, to different degrees with the two leads: Harm and Mac (or in some cases even the actors).
Even with the blatant pro-military stance from the get-go, JAG wasn't Backed by the Pentagon for the first two seasons because the Navy, following the Tailhook incident and the controversy of introducing females on combat ships and fighter planes, were in a hyper-sensitive mode and didn't want to be associated with any TV-show dramatizing crimes committed in the service.
This is all made rather darkly Hilarious in Hindsight due to the show's post 9/11 policy of terrorists being furiously condemned and castigated as the absolute worst of all humanity and those aiding and abetting terrorists (as Harm and Mac happily did in this episode) being held in special contempt, which raises the delightful implication that terrorism is only bad if it is the US being targeted.
Artistic License - Military: When the pilot first aired, a group of real Navy JAG officers got together to watch it. Before it began, everyone agreed to take a shot each time they saw a mistake. The contest had to end before the first commercial break because they knew they'd be passed out unconscious before the end if it continued.
Some fans argue passionately about who was the best female lead: Andrea Parker, Tracey Needham or Catherine Bell. Since Bell starred in 9 out of 10 seasons some people see this debate as moot. Parker was hired for the Pilot episode but NBC did not want her for the series so Donald P. Bellisario was forced to hire Needham. When the show moved to CBS for the second season, Bellisario didn't want to keep Needham, but Parker had already been cast in a lead role in The Pretender and was thus unavailible. Bellisario took a gambit and hired an unknown actress (Bell) who'd had a small role in the last season 1 episode, and the rest is history...
Opinions obviously varied when the comic relief characters Bud and Harriet suffered the tragedy of Harriet giving birth to a stillborn child. Some viewed it as an unnecessarily cruel hand dealt to two undeserving characters while others saw it as a well executed dramatic twist that kicked off dialog on an issue many people are reluctant to talk about in real life.
The sudden retirement of Admiral Chegwidden following season 9.
Central Theme: The military in general, Navy & Marine Corps in particular, represents all thatís good about America, and although there are a few rotten apples in the barrel, they are invariably dealt with, and the military as an institution is never at fault.
A subversion of Armies Are Evil as far as it gets without being outright propaganda.
Complete Monster: Charles "Charlie" Lynch from season 4's "Nobody's Child" and "Goodbyes" is a remorseless psychopath who kills at the drop of a hat for any reason. He begins by stomping a young girl to death solely because he feels she may have disrespected him. After the murder, Lynch opts to target her sister for fun. While initially stopped, he later returns to kidnap said sister and hold her hostage to torment her mentally before he plans on murdering her as well. When questioned about his motives, he states he kills for fun and asks if anyone has a problem with it.
Genius Bonus: Sometimes on JAG, the meaning of military acronyms are never explained to the viewers, and upon rarer occasion are references made to case law without explaining in detail what that case means to the viewers.
Mary Sue: Sarah MacKenzie skirts dangerously close to this. Harm dances back and forth over the line as a Marty Stu too.
If you rewatch the series you'll find plenty of character flaws in Mac. Harm, on the other hand, is more or less an Escapist Character. Earlier on in the show, his somewhat rusty piloting skills are an off-and-on source of humor, such as in "Pilot Error", before he became an Ace Pilot in every flying object he came near.
The Scrappy: Lt. Loren Singer is disliked by a good portion of the fandom.
No doubt intentional, as most of the cast didn't like her much either - she was a lying, manipulative, power-hungry bitch and something of a Smug Snake. And then she died and Harm got accused of her murder in the NCIS pilot episodes. He's lucky Gibbs was investigating...
Vast Bureaucracy: On JAG this tropes comes in two different flavors. If concerning the Navy and Marine Corps, the vast bureaucracy, which it is, will often be portrayed in a positive and/or neutral sense. If concerning any other service or another non-military agency the negatives will be accentuated.
The Woobie: Both Bud and Harriet may qualify for this - Bud especially after the seventh season finale.