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.
Ensemble Darkhorse: Oswald Kittner (JayBaruchel), a fantasy baseball player from "Hardball," was originally going to be another oneshot before fan reaction caused the creators to call him back for "Democracy."
Family-Unfriendly Aesop: In the "Hydra" episode, when our cast decides that when it comes to child custody, the self-proclaimed rights of a surrogate mother trump anyone else's, including the biological parents, and to hell with the contract she signed and what the court ruled.
To be fair, they only made that decision after learning that the biological mother was dead, the biological father was nonexistent, the adoptive father and company were blatantly unsuitable while the surrogate mother and the child genuinely cared for each other.
Lampshaded jokingly by both characters in episodes in the fifth and sixth season. Especially in the sixth season, specifically the episode about the dating bet with Agent Betancourt and in the series finale.
Gambit Roulette: In several episodes the criminals appear to use this. A notable case is the episode which centers around a dirty bomb threat somewhere in LA, which turns out to be fake; the actual point of the threat was to trigger the evacuation of the immediate area, so the crooks could break into a vault without interference. However, the plan requires that the FBI evacuate the right area, which was not revealed by the "terrorists" and which is only determined at the last minute through extreme deductive skill (and nearly incorrectly anyway). Had the FBI guessed wrong, the plan would have failed. Especially since Charlie very nearly did choose the wrong location.
While similar to the plan in Die Hard with a Vengeance in that movie the criminals were smart enough to call in the threat to force the evacuation ahead of time instead of relying on the police to figure out the bomb threat with very little actual evidence.
Ho Yay: In the episode Friendly Fire, Colby, David, and Nikki make a bet on who would show up with the best-looking date; Colby and David win by declaring that they're each other's dates (Nikki lost when her date walked out on her after learning that she was the cop who arrested his friend for public intoxication when he was actually suffering from food poisoning).
At the end of the season, David is leaving for DC and everyone else refers to it as Colby and David's "breakup".
When they're forced to spend time apart, Colby seems to go into withdrawal.
The Scrappy: Nikki. She has a four year degree from the streets of Compton, yo.
Seasonal Rot: In general, the mathematics underwriting the solutions is sound, and explained in such a way as to remain at least a little accessible to viewers. During seasons 1 to 2, the writers were fairly good at keeping each episode theme-focused to illustrate a few related concepts or particular branch of mathematics, allowing them to give the math at least some decent coverage in depth. Unfortunately, as episode number climbed (especially in Season 4), the math degenerated into magical solution generators. The creators gave the series a minor retool around the midpoint of Season 5, now the math has been mostly relegated to a side show, and more personal drama are being pushed in front; most of the episodes in season 6 feature almost no math at all.