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.
Award Snub: The prospect of Courteney Cox headlining another network sitcom drew decent enough publicity, with some finding her performance to be strong for awards consideration. However, to some consternation, she failed to receive any recognition by the Emmys, knowledge exacerbated by the realization that she never received acknowledgment for her work on Friends either.
Big Lipped Alligator Moment: If you don't follow Community, Danny Pudi's brief cameo as an extra who looks into the camera and run off appears to be this. It's actually a plot thread from that show that his character, Abed, is a huge Cougar Town fan, and he was asked to appear as an extra. He's running off because he's pooped his pants from the stress.
Family-Unfriendly Aesop: The episode that reveals Grayson's atheism. The whole episode has everyone in the cul de sac crew against him. Hell, at one point they all pelt him with dodgeballs. Jules wants him to believe for her the same way she's playing dodgeball for him. The whole episode focuses on how he's wrong not to join her in faith when he's not asking her to join him in disbelief. And at the end he prays for her (to win at dodgeball). Just replace "secretly atheist" with "secretly Jewish" and replay the scene where they pelt him with dodgeballs.
At the same time the show does subvert this somewhat, in that Grayson's on the receiving end of all the positive miracles, but Jules is on the bad end; when he says he just doesn't believe, a bird flies into the room and lands on the counter and Jules tries to claim it as her own miracle; and when Grayson prays for her (just thinking good thoughts) not only does his dodgeball team win, it wins because the other team keeps fouling by hitting Jules (the only player left on his team) in the head); when they're sitting on the beach, she's attacked by a cloud of seagulls while he's left alone.
Growing the Beard: Around the fifth episode, the show stopped focusing on Jules dating younger men and began to pay more attention to the entire cast-resulting in a much more enjoyable show.
Season 2 has received a better score on Metacritic (75-positive reviews) then the first season (50-mixed reviews), meaning the show might go from a niche to a well respected sitcom. Season 3 got even better reviews.
Hollywood Homely: She's 41, but she's also Courteney Cox. The only reason she might not be able to get dates is because she's a bit crazy. Though this is probably more averted than anything else as there are several indicators that it's more the crazy part rather than anything else such as supposedly homeliness.
Ho Yay: Quite a bit, especially between Andy and Bobby.
Moreso Andy for Bobby than the other way around, but it is definitely there on both sides.
Invoked between Grayson and Bobby to demonstrate game for Travis.
Les Yay: Ellie and Jules have a ton of this. They're closer to each other than to anyone else, they spend hours talking, they admire how each other look, and they've discussed killing Ellie's husband so they can be together.
Season 3 reveals that Ellie goes commando under her wetsuit, and it's Jules rather than Andy who helps her put it on.
They both keep packed bags in their cars for when they finally decide to take off together.
Also, Ellie likes to kiss her best friends on the lips alot, including her female best friends.
Bill Lawrence has gone as far as to make videos on Facebook's Scrub page to give the show the advertising that ABC hasn't, although he quickly backpedaled out of this strategy and apologized.
Never Live It Down: The show's title, which still gets a lot of flak. Everyone from Bill Lawrence down have voiced that the title should be changed (esp. once the original premise was scrapped), but it was too late in the show's run, and a switch might have doomed the fledging show. So they've turned to lampshading it with couch gags on the title card and episode titles.
That said, some network executives have been on board with changing the title as well. The problem comes in finding one that fits, doesn't conflict with other shows or properties, doesn't completely confuse viewers trying to find it, and so forth.