Antorell the wizard in Patricia C. Wrede's Enchanted Forest Chronicles. His father, Zemenar, is the series' closest thing to a Big Bad (in the first three books, anyway), and Antorell wants to be favored by him, but he — and pretty much everyone else — sees him as largely inept, to the point that the heroes will often talk about him as if he wasn't in the room. He's never really presented as a sympathetic character, and he spends much of his time trying to kill the series' main female protagonist (or maybe not... it's sometimes hard to tell if he hates her, likes her, or both), but he's so bad about it that he's hardly ever presented as a threat, he never catches a break, and is all in all just so pathetic that it's hard not to feel a little bad for the guy.
While Sloan in the Inheritance Cycle has certainly done some terrible things — killing a man, selling out his village to man-eating mooks, and bullying the protagonist in his younger years — it's revealed that he did everything out of love for his daughter, and so lies on a fuzzy line between this trope and Well-Intentioned Extremist.
Toward the end of the sixth Harry Potter novel and through all of the seventh, Draco Malfoy has this role. He's pretty much forced into more important villainous acts that can leave an impact in the existing war (apart from being a male Alpha Bitch and jerk which was what he was good at) by the threat of Voldemort killing him and his parents. Also noticeable is that while in the past, Harry and friends hated Draco, they instead end up seeing him as pathetic, and keep saving him even as he keeps trying to (admittedly half-heartedly) oppose them.
'Evil Harry Dread' from The Last Hero; he purposely hires ineffectual henchman and cheerfully goes through the whole 'evil overlord' schtick. In return he knows the heroes will give him just enough room to escape and let the game begin again.
Bosun Smee in Peter Pan is unhappy about the fact that unlike the other pirates, Peter and the other children adore him.
In the Rainbow Magic series, some of the goblins are this, especially ones that utterly fail at their assigned tasks. Rachel and Kirsty even feel sorry for them at times.
Some of the more incompetent Mooks in the Redwall series fall into this category.
Vaurien Scapegrace from Skulduggery Pleasant. His major goal in life is to be "Killer Supreme". Not only does he not manage to kill anyone until two whole books after his initial appearance, but he ends up being killed himself and turned into a zombie before even that.
The Pharaoh from Soon I Will Be Invincible is a goofy guy with a (possibly) magic hammer and a poor grasp of history, despite being powerful enough to almost kill the local Superman expy with his bare hands when provoked.
Jabba the Hutt may have been a dreaded and feared gangster in Star Wars continuity, but his father Zorba, who appeared in a few Expanded Universe stories, was a big joke. Several years after his son's death, he sought revenge against Leia and Han, but he never even got to Han; his attempts on Leia's life were all Epic Fails. He came closest the first time, attempting to deal her a Karmic Death by throwing her to the sarlacc, but that only ended with him humiliated; not only was he fed to the beast, but it got sick as a result and vomited him out. After barely avoiding starving to death in the Tatooine desert before someone found him, he made other attempts against Leia but they were even worse. He eventually became a recluse, and it's believed he eventually died in isolation.
Prince (later King) Korin, The Dragon (although the Big Bad dies first) of Lynn Flewelling'sTamír Trilogy...although, especially towards the end, he ends up less sympathetic than merely pitiful. In real-world history, kings like him tended to end up with the sobriquet of "The Unready".
The Hundred and One Dalmatians: The Dalmatians originally pity Cruella's husband, seeing him as just as much a victim of Cruella's machinations as they are. Cruella's cat tells them they're wasting their sympathy; he is every bit as evil as his wife, and the only difference between them is that he isn't strong enough to act on his desires, and she is.