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.
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.
Sudanese Ambassador Moshak in "Embassy" as he kills his own people, stole vials ofEbola from a U.S. lab, and when Harm is about to get him he throws at vial of Ebola at him. Fortunately Harm caught it.
In "Act of Terror", Percival Bertram is a wealthy businessman (looking every bit like a Corrupt Hick) who supports right-wing conservative politicians and brands himself as a super-patriot advocating that the U.S. should take gloves of with respect to terrorists to U.S. interests in the Middle East. However, the alleged super-patriot finances terrorism in the Middle East against U.S. interests (supposedly to create a self-fulfilling prophecy gaining his own business interests.)
Serial Killer Charles "Charlie" Lynch in "Goodbyes". In "Nobody's Child" he had offscreen brutally stamped to death a young girl. Harmon Rabb confronts him on a decommissioned navy ship in Philadelphia where he'd taken the twin sister of the killed girl.
Rabb: Charlie, there's something I need to know. Why did you kill Annie?
Lynch: I told her not to get on that school bus.
Rabb: She just wanted to be with kids her own age.
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.
This troper strongly disagrees with the notion that Mac is a Mary Sue: if you rewatch the series you'll find plenty of character flaws. Harm, on the other hand, is more or less an Escapist Character.
Tear Jerker: At the end of season seven, Bud accidentally steps on a landmine, blowing his leg off under the knee. Season eight's opener almost has him die as a result. This is something of a Kick the Dog moment as well, given he was trying to warn a young boy away from landmines that the boy was fully aware of. Kid even tossed a rock at him.
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...
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.
The Woobie: Both Bud and Harriet may qualify for this - Bud especially after the seventh season finale.