In 1942's "Dog Trouble", a proto-version of Spike alternates between terrorising Tom and Jerry until they end up in the same safe haven atop a cuckoo clock. Jerry spots a basket of knitting yarn, and while Tom distracts Spike, he winds the yarn around every piece of furniture and breakable item in the living room, then provokes Spike into running headlong into the tangled web and destroying the contents of the room. An irate Mammy Two-Shoes throws an indignant Spike back onto the porch.
In 1952's "Triplet Trouble", after the eponymous feline hellions have wrought havoc on both of them (while presenting angelic exteriors to Mammy Two-Shoes), Tom and Jerry exact revenge in style. Jerry first provokes the kittens by drinking their purloined cream and spitting it back in their faces, then leads them straight to Tom, perched on a hostess trolley... on which he takes to the air like a bomber pilot, hurling pies and watermelons at the kittens before scooping them up and dropping them onto a spinning clothesline. Jerry spanks each kitten with a carpet beater while Tom ties paper wings to their backs, so that when Mammy returns with a bottle of cream, she finds the "little angels" still spinning on the clothesline, each sporting a bright red backside.
This seems to happen alot in the made for video movies but the greatest example is "Tom and Jerry Meet the Wizard of Oz" Early in the film, Miss Gulch takes Toto away from Dorothy while Tom and Jerry were incredibly saddened by the sight of this and what do they do about it... they fixed a makeshift bike and went after Miss Gulch and managed to save Toto. Then as the film progresses, the two try to protect Dorothy from the Wicked Witch of the West and manage to get the very bucket of water that melts her.
It doesn't just have to be when they team up to defeat an enemy either. Any time they team up counts as a CMOA or a CMOH. In 1958's "Tot Watchers", Tom and Jerry work together to bring a baby safely home (because the Dumb Blonde babysitter is too busy chatting on the phone to notice the baby wandering straight into various dangerous situations).
It can also be particularly gratifying when Tom wins on occasion. When he does win it tends to be because he really deserved to (but once or twice it's just letting the villain win).
In 1944's "The Million Dollar Cat", Tom inherits a vast amount of money, but the inheritance comes with a clause that he will lose all the money if he ever harms a single animal, "Even a mouse". Jerry decides to be a complete prick about this: stealing Tom's money, eating the extravagant food right off of Tom's plate and even causing grievous bodily harm to the poor housecat, all because he knows Tom can't retaliate. Eventually Tom snaps and, after tearing up the contract and stuffing down Jerry's throat, proceeds to beat the crap out of the little rodent, because there are some things more important than money. Like the happiness you gain from taking revenge on the little bastard that made your life miserable.
In the 1953 short "Mouse for Sale", after Jerry charms Tom's owner, Joan, as "Jerry the Dancing Mouse" despite Tom's repeated attempts to prove that Jerry is not the rare white mouse Joan believes, Tom turns the tables on Jerry by painting himself white and winning Joan over as "Tom the Dancing Cat", ending the cartoon with a performance that involves repeatedly stomping on Jerry.
In "Timid Tabby", Tom and his cousin, George, team up to mess with Jerry and drive him to believe he's gone mad, sending him running to a house for mice who've had nervous breakdowns.
In "The Vanishing Duck", Jerry and Quacker use vanishing cream to literally turn themselves invisible and just be dicks with Tom. Tom discovers the cream himself and decides to employ some Laser-Guided Karma.
The canary saving Jerry from being run over by Tom in "Kitty Foiled".
In "Professor Tom", when Tom starts spanking his student for letting Jerry get away, Jerry responds to this by breaking Tom's tailbone.
In something of a role reversal episode, "The Little School Mouse" has Jerry trying to teach Nibbles how to outsmart Tom, who sees through him and defeats him each time. Nibbles tries merely politely asking for Tom to assist in tasks, and succeeds.
In "The Milky Waif," Jerry going Papa Wolf on Tom after Tom spanks Nibbles with a fly swatter.