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.
Harsher in Hindsight: In "Permanent Wave," Sam has to save a boy that witnessed a man being shot to death in a matter involving drugs. The character's name was Phil Hartman. It wasn't too many years later when actor Phil Hartman was himself shot to death by his wife, who had a drug problem.
Doubly funny as he's saying this to Sam. A few years after Star Trek: Deep Space Nine ended, Hertzler appeared in the Star Trek: Enterprise episode "Judgment," where his character and Archer discussed honor and Archer helped him rediscover his own sense of honor.
In "All Americans", Al mentions that he's watching Super Bowl XXX and that the Pittsburgh Steelers are trailing by three points. Jump head six years to the real Super Bowl XXX, where the Steelers were playing and did trail by three points until a miraculous comeback in the final minutes.
It Was His Sled: Al being the one that Beth leaves for another man in "M.I.A.". It's such common knowledge among fans that you'd forget that the way the episode is structured, it's supposed to be a twist - with Sam stumbling upon a picture of young Al in Beth's home about halfway through.
Actually, the audience is informed of this before Sam is with Beth introducing herself to Dirk as Beth Calavicci early on.
Marty Stu: Sometimes Sam's absolute purity of heart and expert knowledge in everything from music to martial arts to several branches of science put him into this category.
Narm: When Lee Harvey Oswald sees his face in the Waiting Room (actually Sam's face), he understandably freaks out... but we cut to Sam, mouth open, with Oswald's slightly-deadpan scream pouring out.
They Changed It, Now It Sucks: On the DVD releases, a large number of the original songs were changed for copyright reasons (the songs were usually well known songs from the time period that a particular episode is set it), which caused a HUGE backlash from fans. In particular, the last episode of the second season, "M.I.A.", removed Ray Charles' "Georgia On My Mind" with some generic muzak, ruining what many thought was the best moment of the entire series (Al, in hologram form, dancing with his first wife who left him while he was a POW in Vietnam). This is definitely a instance in which Tropes Are Not Bad.
The Season 5 theme song, meanwhile, wasn't very well-received by fans.