--The bastardized Beatrice and Benedick romance. The sassy female protagonist loathes on sight the arrogant insulting cruel vindictive dirtbag male (but secretly can't stop thinking about him cause he's just so dreamy), and they try to kill each other, literally or figuratively, throughout the story. Yet it turns out, under that crusty evil exterior, the guy's just really an old softy with a heart of gold. And they go from loathing to wedding or bedding within about 4 pages. For examples see 80% of all YA fiction, 60% of all urban/paranormal fantasy, and 100% of all romance.
--As an extension of that bad boy thing, how in period pieces, there's a tendency to Byronify the male hero as much as possible, and make him all brooding, glowering, and mysterious; even if the original character bore very little resemblance to such a character.
--Misery lit and putting characters through every single possible tragedy imaginable without a single ray of hope anywhere.
--The wish fulfillment characters, most notably embodied in the Bella Swann types. If not only the character, but also the narrator, mention almost every other page about how ordinary or plain or awkward or unremarkable she/he is; and the character as written also has zero personality, charm or common sense and is often also self-absorbed in the extreme; don't make every character of the opposite gender fall madly in love with them. Seriously. If your character has all the personality of a rock, and on top of that is whiny, self-obsessed, vacant, and supposedly unattractive--is everyone really going to be falling all over themselves to get with them?
--How many writers have what's touted to be a "feminist" work but their work is only feminist in that it passed a feminist in a subway once. And they can't create their main heroine without making her extremely pushy, shouty, nosy, lacking in any tact or empathy whatsoever; and she must always suffer a huge comedown where she learns her place by ending up in humiliating and humbling circumstances because of her meddling or her reaching outside her sphere.
--The next time I see an female superhero, fighter, police detective or other active profession doing their jobs in high heels and especially stilettos, I can't be held responsible for my actions.
--Protagonists who have never fought or have any training whatsoever going up against a whole gang to bringing them all down single-handedly. Or additionally, a hero/heroine who has never had any magic training or used their magic before managing to save the whole world through their powers.
--The glamor fatal illness, where the character grows more and more radiant and beautiful as they die.
Any others to add?