Though there are a lot of shows/book/manga/the like that I enjoy, I'm iffy about joining a fandom. Due to my tendency to gravitate to ships that have a darker/conflicted past, I often find myself enjoying pairings that are considered by the masses as 'horrible'.
Ships such as Nnoitra/Neliel (Bleach), Sasuke/Karin (Naruto), Dave/Kurt (Glee), Jesse/Rachel (Glee), Rudy 3/Jess (Misfits), Mai/Zuko (A;TLA), Murtagh/Nasuada (The Inheritance Trilogy), Draco/Hermione (Harry Potter), Heymitch/Effie (THG), Conrad/Doc Worth (HiNaBN), Hikaru/Haruhi (OHSHC), Terra/Beast Boy (Teen Titans) happen to get me in trouble when I express my love for them. I can understand a lot of the hate for most of these ships as people have an emotional connection or a similar experience, but it's something I find people take far too seriously. I ship because I enjoy the dynamics and connection between the couples. Other people ship for the same reasons, only with different pairings. We read situations differently and are attracted to different things.
There are ships that I don't like, but I have plenty of friends who do ship them. It's something we can get over, discuss, and appreciate. But, according to some of the more hardcore 'fans', that's impossible. Apparently if you like a show, you can only befriend people who like the same couples in it that you do :/
So, I like to scratch the surface of a fandom to the point where I can enjoy it, but I can't delve too far into it if I don't want my interests to be attacked. It's sad seeing as we should be able to enjoy it.
That being said, I do enjoy some popular pairings. Bubblegum/Mareline (Adventure Time), Ichigo/Orihime (Bleach), Naruto/Hinata (Naruto), Nathan/Kelly (Misfits), Rogue/Gambit (X-Men), ships that are considered 'acceptable' to a fandom. Even then, you still get criticism for being too obvious and only liking 'shallow' pairing because they're popular. No matter what ship you like, you're going to be judged for your choice. There's no way to make a whole fandom happy.
In the Glee fandom, I find Kurtofsky Pirates and Klaine Trainers are often at each others' throats. Yet I met someone through the fandom who was a Klainer, and she's one of the most awesome people I've met. Really, when I meet someone who enjoys the show I like, what they ship isn't exactly the most important thing to me. If you like a show, awesome! I do too! Shipping isn't the center of every story. Everyone gets so worked up with ships that I think they forget these are fictional people.
I don't ship Ronmione, but I'm not going to chuck a hissy fit because it happened. I'll go to fanfiction to get my Dramione/Krumione fix instead. I can still enjoy the book/movie for what it is.
I do ship Maiko/Kataang, and it's canon, but I'm not going to force it down the throats of everyone who ships something else.
What's canon and not canon doesn't make one ship more 'right' than the other.
As for shipping animal like creatures, I see nothing wrong with it. I don't like or promote the sexual aspects of it, but I don't mind romanticism. It happens in a lot of shows, such as Pikachu and Buneary. It's not prominent, but it's there, and the majority don't see anything wrong with it. If someone were to say they shipped animals in a show, I wouldn't bat an eye. I ship Gay and Lech in Bear Nuts. It's not something I view in a sexual nature, more I like their personality clashes and how they interact. I've never seen MLP, and I'm guessing a lot of the fandom do take it far and sexualize it. Whatever their reasons for doing so, I don't care. It's their ship and their interest, and though I find it a little irksome, it really has nothing to do with me. Let shippers ship. It's none of my business what another person ships, whether they're animals or humans.
I have nothing against M-rated fanfiction. In fact, I prefer it. I prefer darker stories. Strolling the G/Pg/t rated stories don't give me that. M doesn't always mean sex. Take a show such as Adventure Time that's aimed at children and keeps a cartoonish air to it. Looking through the M-rated section, I can find deeper and darker versions of the same show. That being said, I don't mind smut in a story. I don't seek out smut on its own, though I believe there's nothing wrong with it, but a well written story that has sexual scenes is fine with me. I've stumbled across smut of childrens' shows, and it's never aimed for the kids to read. There's a story, that is personally one of my all time favourite works of fanfiction, that places and older Sid and Andy from Toy Story together. It's something I'd never thought of, but the way this person wrote it made it seem so natural. If you don't want to see a show you watched as a child in a different light, don't stroll down the 'romance' fanfictions.
I think people view sex to be a dirty subject, which I disagree with. I write M-rated fanfiction. I haven't written anything below that rating for years. I don't like reading or writing purely bubbly or happy stories. I like heartbreak and adversity. That doesn't mean I don't like a happy ending, I do, but I like a sense of reality and hardship hardwired into the storyline. Because of how scary the fandom can be, I tend to stick with reading fanfiction and that's it. I don't like going further than that. But if a story takes ship/character bashing into the story and completely OOCs characters because the author dislikes them, I can't enjoy it anymore. Even if I dislike a character, I can't bash them in a story. It feels disrespectful as anyone who reads it may like the character.
I also find pregnancy to be a major storyline killer. I've seen a lot of great stories just die because BAM! YOU'RE PREGNANT! Especially if there's a supernatural aspect to it that causes the baby to develop and be delivered super fast. No. Just... no. Some people can pull pregnancy stories off well, and I respect that, but most I find do it to force two people who don't particually like each other to work together. It's a bad way to force a ship. Recently, I was reading a Nnoitra/Neliel story that started off strong, then pulled the 'super fast pregnancy' card and ruined it.
For yaoi/yuri/slash, I don't really ship couples due to their gender. I ship because of their dynamics despite gender. I know some people find same-sex couples hotter, and I understand that, but it's not about what's 'hot or not' to me. If I like the interactions and chemistry between two characters, I'll ship them whether or not they're male or female.
As for what fandoms I'm kinda-sorta-not-really-but-I-like-the-show 'in', I'm pretty sure I've already listed them all above, but I enjoy:
Misfits, HiNaBN, Glee (to a certain extent. A lot of it bugs me too), Bleach, Naruto, Fruits Basket, Death Note, Adventure Time, Narnia, The Inheritance Cycle, Ouran High School Host Club, Elfen Lied, American Horror Story, 2 Broke Girls, X-Men, Big Bang Theory, A;TLA/A;LOK, Teen Titans, THG, Pokemon, Digimon, Rise Of The Guardians.
Long list, and I'm probably missing some, but I have no life outside of work :\