Mousse from Ranma ½ is a loser whose plots against Ranma go only so far before backfiring spectacularly. He's usually played as an unrepentant jerk, although maybe once a season, he'd get a moment of quiet reflection for the audience to sympathize with him — right before going back to his old ways, naturally. Both the ineffectual and sympathetic aspects are ironic, because Mousse is the most ruthlessly homicidal of Ranma's regular rivals. By contrast, Mousse spends most of the series willing to do just about anything to kill Ranma, routinely using bladed and impaling weapons and attacking with ambushes. He even comments once on being willing to slip poisonous mushrooms into Ranma's food.
Principal Uchimiyada on Great Teacher Onizuka often plots to get rid of Onizuka, and yet is portrayed as less of a threat than the troubled students in Onizuka's class, like Miyabi, Urumi, and (towards the end of the manga) Sho.
Meowth as well. He is one of the weakest battling Pokemon in the series, thus spends the large majority of the time assisting with the duo's zany schemes and blabbing his mouth off rather than face an inevitable curbstomp.
Meowth had an excuse. He spent so much time when he was young learning how to talk that he let his natural skills and powers as a Pokémon degenerate. He may be a poor Pokémon in terms of battles, but being able to talk (and translate the language of other Pokémon for his two partners) does occasionally have advantages. (Disadvantages too. He was kidnapped by Hunter-J once because she felt a talking Pokémon was worth a bundle.)
Martina, the anime-exclusive Guest Star Party Member and fallen princess from the second season of the Slayers anime, who only knows how to perform minor curses and can't defend herself at all. She spends the first half of the season trying to get revenge on Lina and her friends for destroying her home, and fails every time; after that, she decides to tag along with them. She doesdecide to help Lina out morally during the final battle, though.
Dorodoran in Futari Wa Pretty Cure Splash Star. Unlike most Pretty Cure villains, he's trying as hard as he can from the start, and is increasingly frustrated and upset by his repeated failures. When he finally comes close to victory, it all evaporates due to sabotage by Michiru and Kaoru. It's hard not to feel sorry for him.
Zeta Gundam had Jerid Mesa, who ended up becoming the Designated Rival for the show's protagonist, got into a vicious cycle of each killing the other's friends and/or lovers in battle, and eventually was killed when the hero threw his mobile suit into an exploding battleship.
Gundam 00 had Patrick Coulasour, an ace in 'simulated' combat, who quickly develops a one-sided rivalry with the Gundams after being publicly humiliated by them in the first episode, only to be dispatched in a similar fashion when he returns later. As with Jeremiah, fans latched onto him, giving him the nickname "Team Patrick". He eventually latches onto his commanding officer, Kati Mannequin, and goes on to be shot down another 5 or 6 times, even after switching sides.
Jeremiah Gottwald from Code Geass, who began the show as the military equivalent of a Jerk Jock, but made the mistake of crossing Lelouch, which left him disgraced, hated, and saddled with the ignoble nickname "Orange". His enormous popularity spared him from a planned quick death, resulting in his returning later as an Ax-Crazy cyborg. Just to crank up the sympathy another few notches, the side materials revealed that Jeremiah was a palace guard on the day Empress Marianne was killed, and based his entire career on an attempt to atone for failing not only Marianne, but her children, who disappeared in Japan, leading him to think that they were killed by the Japanese, which prompted his racism against Elevens, which resulted in Lelouch (Marianne's supposedly-dead son) publicly humiliating him. Whoops...In the second season, Jeremiah was sent by the Geass Order to assassinate Lelouch, revealed that he was still loyal to Marianne, and when Lelouch admitted that avenging his mother was one of his main reasons for becoming Zero, "Orange-Boy" immediately dropped his thirst for vengeance and became Lelouch's retainer.
Excel in Excel♥Saga at times. She really wants to help her Lord Il Palazzo's plans to take over the world, but she fails so badly at every mission given to her. Often subverted though by following a sympathetic moment with doing or saying something disturbing.
Viral from Tengen Toppa Gurren Lagann, who does not have Spiral Power like the protagonists and thus can only watch as they reach ever increasing heights of power. By the time the heroes reach the Spiral King himself, Viral, even given immortality and a four-armed upgrade to his Humongous Mecha, is swatted aside by Simon as if he is a humorous interlude.
Harry Champ from ZoidsNew Century, though he's more of a rival than a villain per se. Major Polta is certainly ineffectual, but does very little to garner sympathy aside from kidnapping Leena.
There's also the Zabre Fangs; though they do prove to be worthy opponents a few times in the series, they're mostly comic relief, and, in fact, lose their final battle against the Blitz Team when their Zoids do a facefault and malfunction from the fall.
Kinkotsuman and Iwao from Kinnikuman are complete losers, plain and simple, who can't seem to do anything right. Of course, they're also kind of a subversion, because Kinnikuman is just as big a loser. Also, sometimes, when they aim high, they miss high. Like when Kinkotsuman accidentally shot Terryman in the leg when he was aiming for Kinnikuman, and Terryman ended up having to have his leg amputated (this is only in the manga, since in the TV series, Terryman eventually gets better, but the toned-down anime scene still is sad for poor Terryman).
In fact, in Nisei, Kinkotsuman's son, Bone Cold's, entire motivation as a villain is distancing himself from how lame his dad was.
Only once does Pilaf (almost) get what he wants...he manages to successfully get a wish from Shen Long in the first episode of Dragonball GT. However, instead of wishing for what he wanted, he shouts in frustration at Goku (who showed up just as the dragon was summoned) "I wish you were a kid again!" - not as an actual intended wish, but because Goku was so much easier to defeat as a child.
Japoli, Katejin, and Enge, the Punch Clock Villains of Overman King Gainer who are completely incompetent in their jobs, and are only a threat if they have Overman. They are the main source of comic relief with the Siberian Railroad.
Lilynette, Stark's Token Mini-Moe fraccion from Bleach. She's currently fighting Ukitake, who is one of the 5 most powerful shinigami in existence. The fight so far has consisted of Ukitake telling her that he doesn't want to fight a little girl and simply deflecting or dodging every attack she threw at him. Currently, he's playing keep-away with her Zanpaktou as she cries at him to give it back and threatens over and over again to kill him.
And then she merges with Stark and they descend into full out loner Woobie territory — turns out, Lilynette is Stark's Imaginary Friend turned real due to sheer loneliness.
Or Stark is her Imaginary Friend. He states for both of them that they've been together so long that he can't even remember who is the real one anymore.
Ukitake even lectures the girl on how her determination is admirable, but she simply lacks the ability to 'fight' him properly (i.e take the sword back). She fires a cero, he deflects it with his hand. No wonder she was pissed off.
Also from One Piece is the Laughably EvilGonk, Foxy the Silver Fox, particularly in the anime where he gets more screen time. He's relatively Weak, but Skilled and has only built up such a large crew because he won them in games stacked in his favor, but they seem to genuinely enjoy serving under him because of the fun carnival atmosphere of the Davy Back Fights.
Buaku from Dominion Tank Police and his sidekicks, the Puma sisters. They've always been wannabe Magnificent Bastards, but they were slightly more competent in the manga. Granted, their failures are rarely their own fault, discounting their lack of foresight.
Heavy Metal L-Gaim's Gavlet Gabre is a particularly jarring example. He's introduced as the primary rival, but never once defeats the protagonist, Daba Myroad. During the final battle at Sveto, he fails to defeat the unimportant and generic villain Rockley Ron, which makes the later the sole villain who makes it out of the show without being captured or killed.
In Baccano!, this spot is owned by Dallas Genoard, who isn't all that sympathetic, but is more than ineffectual enough to make up for it.
Many a member from a Quirky Miniboss Squad in the Sailor Moon anime falls into this trope. The noteworthy examples are Jadeite from the Shittenou, Ail and En from the Maikaju filler arc, Eudial and Mimette from the Witches 5, the Amazon Trio, and both Sailor Iron Mouse and Sailor Aluminum Siren from the Sailor Animamates.
Kurumi, Kurumi, Kurumi. As of the end of the anime's first season, she still hasn't caught a break despite confessing to Kazehaya and tearing down what was left of her fake persona — or if she has, it was offscreen.
Keroro from Keroro Gunsou probably counts. His schemes to conquer Earth always seem to end in disasters of some kind, when he's not being sidetracked saving the world from other alien invaders or something.
King Dedede in Kirby of the Stars is the kind of guy who wants respect from the Cappies, and just wants to beat up Kirby for the sake of it, which is why he buys Demon Beasts/monsters online from Holy Nightmare/Nightmare Enterprises. Of course, Kirby always wins the day, so Dedede never gets the respect he wants. To be fair, Dedede isn't really all that bad, he's just mean, misunderstood, and a completely incompetent half-wit.
In Yu-Gi-Oh!... Gee, were to start? Insector Haga and "Dinosaur" Ryuzaki were probably the most well known examples. You kind of felt sorry for them after awhile. Their worst humilation came during the KC Grand Prix when they dueled Zigfried two against one, and he beat them both... On his first turn. (Granted, Zigfried is a guy who gave Kaiba one of the most epic duels of his career, but still...)
Not that there weren't others. There was Jean-Claude Magnum (a Hopeless Suitor to Mai, and a Miles Gloriosus) the unnamed Rare Hunter called "Seeker" by fans (half of Yugi's dialogue during the duel consisted of "The Reason You Suck" Speech) and Gurimo from the DOMA arc. (If you've only seen the dub, that would be the first duelist seen using the Seal of Orichalcos; the dub didn't think he was worth a dub name.) Seriously, Gurimo not only used one Artifact of Doom (The Seal of Orichalcos) he was dumb enough to combine it with a second one (Obelisk the Tormentor). The only thing that was truly surprising about his loss to Yugi is why all the other characters found it so surpising!
Moving to Yu-Gi-Oh! GX; almost every Obelisk student shown as an antagonist except for Manjyome, Asuka, Fubuki, and Kaiser qualifies. (Clearly, most of the students there did not get to the best dorm based on merit.) Others villains like this included Seven Stars member Abidos III who was a participant of the original Shadow Duels of Egypt and undefeated - but only because his servants let him win and the Duel Spirit Don Zaloog (not a bad duelist, really, but not a good villain, he and his gang tried to steal the Shadow Gate Keys, which was pointless, because they wouldn't function unless you won them from the owners). Several antagonists from filler episodes qualify too, and are too numerous to list.
You really can't help but feel sorry for Clawdia after all the times that she fails throughout the series, especially when King Gorge attempts to kill her for failing him for the last time. Luckily, Chase and the gang were there to stop him and chase him off (as he would've completely killed her off if it weren't for them returning her to her old self and redeeming her through Chase's tasty cooking).