All of these are in my own opinion. The article is not about the actual quality of the songs, but more of their use in the show. A short note is included after the title to note the main issue(s). "Done intentionally" means that the faults were acknowledged in the show.
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1.    Cell Block Tango - Poor song choice and offensive; done intentionally. The girls just found out that someone is in an abusive relationship. This was probably one of the worst songs they could have chosen to sing. As said in the show, it was by a bunch of violent, crazy women who killed their significant others over anything from cheating to chewing bubblegum.
2.    Girls Just Wanna Have Fun - Poor song choice and offensive. The song was beautifully done but there’s some problems with the meaning. This was sung to a lesbian who had just been outed, by someone who had taken a part in that. The feministic view lacked and it strongly implied that being a lesbian is just girls just having fun, which is very offensive.
3.    I Kissed a Girl- Poor song choice and offensive. Santana and the girls sang the song to cheer her up and show their support. However, the meaning of it is that kissing girls is a way to look hot and get guys.
4.    Afternoon Delight- Poor song choice; done intentionally. Emma had the Celibacy Club sing this without knowing what ‘Afternoon Delight’ meant. Everyone else picked up on it but it was revealed that she thought it was about dessert, which has nothing to do with promoting celibacy.
5.    Ben- Poor song choice. The song is about a psycho rat who ate his owner.
6.    Jesus is My Friend- Offensive performance; done intentionally. The song was done to pander to the judges, but the performance was offensive. The song is obviously singing about Catholicism and the performers made a distinctive Star of David formation at the end (which is a Jewish symbol).
7.    With You I'm Born Again- Offensive performance; done intentionally. Rachel and Finn purposely paired the song with nun and pastor costumes. This is offensive because people of the church are under a vow of celibacy.
8.    Black and White- Poor song choice. The New Directions sing this to the Warblers to prove their superiority in understanding the meaning of Michael Week. The song is actually about overcoming racial barriers.
9.    Big Ass Heart- Offensive; done intentionally. The whole song is a direct reference and insult to Lauren’s weight. It’s confusing how she enjoyed this but not ‘Fat Bottomed Girls.’
10.    Fat Bottomed Girls- Offensive; done intentionally. Paired with ‘Big Ass Heart,’ it seems like the only songs you can sing to an overweight person must be centered around their weight.
11.    You Keep Me Hangin' On- Poor song choice. If you look at the meaning of the song, it’s inaccurate with Quinn’s storyline. In the show, she was frustrated with trying to keep Finn from being with Rachel and vice versa. The song suggests that someone is hanging on to her in a relationship she wants to end. Since she took charge in their relationship, she could break up with him and he’d be out of her hair in a heartbeat.
12.    The Rain in Spain- Poor song choice. The song was used to teach Puck geography, but several of the lines in the song are not accurate. The rain in Spain is in the mountains, and there are no hurricanes in Hertford, Hereford, or Hampshire. Instead the lines are vocal exercises.
13.    Do They Know It's Christmas- Poor song choice and possibly offensive. The song is about the underprivileged people in Africa being too poor to celebrate Christmas as people in first world countries do, and instead just need to fill their basic needs. The New Directions singing this to people at a homeless shelter would basically be singing to the poor about how poor they are.
14.    Trouty Mouth- Offensive; done intentionally. Here for obvious reasons; the whole song is just insults about Sam’s lips.
15.    Somebody That I Used to Know- Poor song choice. The song is a break-up song but in the show it was sung by two brothers because Blaine didn’t like his brother taking the spotlight and being rude to him.
16.    Smile (Lily Allen)- Poor song choice. Rachel just used it for her and Finn to practice, and it doesn’t relate to their relationship at that time. It’s about a woman being happy over her exes’ misery and attempts to win her back. Finn and Rachel were happily friends and Finn was dating Quinn.
17.    I'm Still Standing- Poor song choice; done intentionally. The use of humor and irony here was unrealistic and in bad taste as it was sung by two people in wheelchairs, and one who had just returned that way from a bad accident.
18.    Tik Tok- Poor song choice. The goal of the week was to find a song that did not glorify drinking alcohol, and this did just that. The only reason the Alcohol Awareness Week pep rally was successful was because people accidently threw up during the performance.
19.    Jessie's Girl- Poor song choice. Similar to ‘(You’re) Having My Baby,’ it was both a good and bad choice. It fit perfectly with the storyline in the most literal sense, but for Finn to sing it made it awkward and offensive to Rachel and Jesse.
20.    Saving All My Love For You- Poor song choice. It was strange for Quinn and Joe to sing this. Their relationship came very abruptly and it was confusing because they never actually announced if they were dating, either before or after.
21.    River- Poor song choice; done intentionally. Paraphrasing what Artie said, in another example of Glee making suicide jokes, the song was just very depressing and not fit for the Christmas special. It really had no place in the episode.
22.    Fighter- Poor song choice. This was another Blaine and Cooper song and it’s here pretty much for the same reason as ‘Somebody That I Used to Know.’ Not only are they not lovers (as the song was about exes), but the whole conflict was minor in retrospect. It almost seemed like an overreaction to the plot.
23.    Isn't She Lovely- Poor song choice; done intentionally. As Mercedes said, the song was about a baby. It was still a sweet song, though.
24.    Glad You Came- Poor song choice. They probably didn’t know since the band didn’t announce it until after the episode, but the song is about orgasms and not a good choice for a competition piece.
25.    Only The Good Die Young- Poor song choice. Of all the times Puck could decide to continue singing songs by Jewish artists, he decides to sing this the week that Kurt’s father has a heart attack. It’s either an unfortunate coincidence or a poor use of foreshadowing on the show’s part.
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A poll for this set of songs can be found link.