Missi from Misfile is hated for getting between Ash and Emily. Current sentiment on the Misfile forums is that Missi should die in a car accident, preferably one involving a steep cliff. It doesn't help that Missi has moved from Romantic False Lead to the Stalker with a Crush. It also doesn't help that the characters are obsessed with racing cars along steep cliffs.
Boy Meets Boy Cy/Skids shippers were definitely furious at Ronnie's existence. The character appeared at the height of the Cy/Skids tension, after it was revealed that Cy did indeed have feelings for Skids. The relationship between them is never resolved and Ronnie, an anime fangirl who wears a Duo Maxwell braid and pulls the interest of both boys seems to be an intentional play on this trope.
Ironically, in spite of the author hanging a lampshade (see page image - there's actually an earlier strip that does a similar Lampshade Hanging too!) about how Cy/Skids shippers would not be happy about the revelation that the one Skids loves is Harley and not Cy, the shippers recognized that Harley was happily together with Mikhael and would never actually hook up with Skids (and that, y'know, Harley/Mikhael is the main couple of the series). They saved their wrath for Ronnie, the character who posed a genuine threat to Cy/Skids.
Within the Megatokyo fandom, the Piro/Kimiko shippers tend to do this to Miho. Similarly, the Miho/Ping shippers give this treatment to Piro.
Amusingly enough, Miho/Piro shippers tend to do this to... Piro again, who they consider an insensitive Jerkass who constantly rags on a completely innocent girl, but should get with her anyway.
Nearly all of Davan's girlfriends suffer this at the hands of the die-hard Davan/PeeJee shippers. This may be justified in the case of Eva (who is revealed to have cheated on Davan with no less than four people during their relationship), but is completely uncalled for in the cases of Branwen and Vanessa. Not so much in the case of Lynn, but that's probably because she barely received any characterization at all, and was explicitly only in it for the sex.
Word of God says that Vanessa was supposed to be introduced after Branwen left, but this storyline was (very) delayed in order to avoid the probable hate.
And the vitriol toward Vanessa is completely unjustified, considering that PeeJee is the biggest Davan/Vanessa Shipper on Deck in the comic itself.
Most Marten/Faye shippers took the sinking of their ship rather gracefully, thought there still seem to be a few that are somewhat bitter towards Dora.
And now that Dora's out of the picture, Angus is probably next in the crosshairs so as to put right what once went wrong.
"Somewhat bitter"? The forum pretty much turned into the Dora Hate Club after she hooked up with Marten, blaming her for everything that went wrong that was even vaguely connected to their relationship, and in a comic where every other character was internet-psychoanalyzed to give them a reasonable, sympathetic explanation for their actions (possibly with the exception of Sven, Dora's brother), the explanation for Dora's behavior was always analyzed as "she's a mean stupid bitch". Even ending the relationship apparently hasn't helped... apparently the lust for blood will only be sated once Dora has been Killed Off for Real.
In Housepets!, Peanut/Grape (typically referred to as "Grapenut") shippers do this to their respective current canon squeezes, Tarot and Maxwell. There's also a King/Sasha ship ("King of Hearts") that does this to Sasha's on-and-off boyfriend, Bino.
"King of Hearts" has given way with King's relationship with Bailey. Now there's a growing tide favoring Sasha with Fox.
A meta-example occurs in the Eurekon arc of And Shine Heaven Now, when Xuanwu (author of Strange Candy and wrote the original plot of Eurekon) tried to convince Erin to kill off Mamoru so Usagi could be paired with Seiya instead. Erin didn't go for it.
In the Homestuck fandom, an artist was recently run off Tumblr entirely because he happened to like and draw (completely tasteful) John/Karkat and large crowds of people disagreed with his choice of ship; in the leadup to the departure said artist lampshaded the hell out of this by drawing a series of pictures of "acceptable ships" as part-peace offering, part-Take That. In general the Homestuck fandom has previously been reasonably devoid of this trope (or at least people are generally respectful enough to not blow it out of proportion), but it's only a matter of time before things like this incident happen more often.
Poor, poorEquius. A small, yet vocal part of the Sollux x Aradia shippers hate him with a passion. Some going as far to call him abusive just so Aradia will get together with Sollux.
There's also a lot of hate towards poor Jane simply because she gets in the way of the fandom prefered Dirk/Jake ship. People were actually cheering when she was confronted about her feelings and managed to screw things up. The girl just can't seem to get a break.