Zenigata's obsessive pursuit of Lupin tends to make him very unsettled whenever Lupin is actually caught, although this is always temporary. He becomes convinced that Lupin wanted to get caught and was trying to Get Into Jail Free. (He's right, of course) One Chance to Breakout is an example from the Green Jacket series.
Invoked in real-life: Goro Naya (the voice of Zenigata) provided a short eulogy (in-character) at the funeral of Yasuo Yamada (the voice of Lupin): "Hey, Lupin, from now on, who should I keep chasing after?” His angry voice shook with tears.
At the beginning of YuYu Hakusho, one of the things that convinces the stuck-in-limbo Yuusuke to come back to life is his rival Kuwabara's tearful bellows to 'come back and fight him' at Yuusuke's funeral.
Although most likely never taught the philosophical and spiritual side of Martial Arts in her training, Triela of Gunslinger Girl solemnly and sadly returned Pinocchio's treasured key-ring to him after slaying him in single combat, paying her final respects to a fellow warrior.
Nagi in Tenchi Muyo!'s Universe continuity does something like this in the final episode after Ryoko's apparent death, though she's also noticeably skeptical as they Never Found the Body.
Technically, they were supposed to be on the same side, but since they spent the majority of their mutual appearances trying to take each other out, Alucard's visible distress as Father Anderson dies in the Hellsing manga likely qualifies. Justified in that it seemed he'd been hoping for Anderson to be the one who's finally able to kill him.
In Legend of Galactic Heroes, most of the top ranking officers in the Imperial Army, and Emperor Reinhard, mourn for Yang Wenli.
Yang also mourned for Siegfried Kircheis, saying he felt like he'd lost a friend.
In Death Note, Light feels a profound sense of boredom, if not outright loss, when he finally defeats L, and considers L's successor Near as not worthy of taking up the mantle.
Initially however, Light is ecstatic to have beaten him, literally dancing on his grave in the compilation special. It's only after a several year timeskip of basically having the world in his pocket that he starts missing him.
In Guyver, Aptom actually watches over the friends of his rival Sho for a year, to the point of absorbing/eating other Zoanoids so he'd have a reason to return.
This trope gets played with in the case of Buggy. After Whitebeard dies, he flees crying (mainly because he's scared witless). His current crew, however, sees his tears as invoking this trope.
Played straight in Chapter 0. Shiki, Big Bad of Strong World was once one of Gold Roger's pirate rivals, but hoped We Can Rule Together. He was outraged to learn that the navy had arrested Roger and was planning to execute him in the East Blue. After the Great Pirate Era starts, we go to Shiki's cell in Impel Down where he's flat on his back, angsting over Roger's death and refusal to join him.
In Transformers Armada, Megatron seems to be genuinely upset when he finally manages to kill Optimus Prime, and acts a lot more like his old self after Prime gets better.
After Cell is defeated in Dragon Ball Z, Vegeta is so distraught at Goku's death, that he vows that he'll never fight again.
MW has Michio crying over Garai after he sacrifices himself with the titular gas to the ocean.
In Episode 93 of Kirby of the Stars, Dedede gets a big surprise when he learns that his latest prank, which involved exploding watermelons, "killed" Kirby, and that everyone in Cappy Town is having a "funeral" for him to remember his time in the village. Dedede and Escargoon become upset and start crying like babies over Kirby's "death". Dedede places a watermelon at Kirby's "grave", and then Kirby pops back out and eats the watermelon, and Dedede becomes overjoyed and hugs Kirby in realization that Kirby was alright after all.
Parodied in Tentai Senshi Sunred, when Vamp goes through this after Sunred becomes seriously angry at him and drops their normal relationship in favour of not talking to him. The irony is that their 'normal' relationship is Sunred being constantly (and openly) annoyed at him anyway, which Vamp cheerfully seems to accept as Sunred just being Sunred.
Happens to Kira after he destroyed the Desert Tiger's mobile suit. That's when Cagalli had to comfort him.
Also Rau briefly in the final episode. Having only damaged Mu and letting him escape (probably so he can witness his apparent triumph later on) he looks genuinely shocked and disappointed when he comes across the remains of the Strike shortly afterwards since Mu ended up taking a hit for Archangel. Though he quickly gets over it and proceeds to attack Kira and rant at him instead, this shows that Rau thought of Mu as his Worthy Opponent unlike Kira who he thinks is an inhuman abomination. Also, Mu and Rau are more or less brothers, something Rau knew all along but Mu had only recently discovered.
During the "Funeral for a Friend" arc which followed Superman's death, there was a one panel shot of Toyman mourning the death and admiring Superman's kindness to children.
Rorschach sees Moloch visit The Comedian's grave at the end of the Watchmen chapter "Absent Friends".
Rorschach: Is that what happens to us? No time for friends? Only our enemies leave roses. Violent lives ending violently.
Subverted in Captain Atom #50: Wade Eiling seemed genuinely sorrowful at Dr. Megala's death, but it soon turned out that he was just upset that Megala's death would trigger the failsafe that would reveal all the dirty secrets of the Captain Atom Project to the American public.
Civil War: The Confession is entirely about this. The fact that said antagonist was formerly best friends with the dead hero and never intended him to die just makes his victory all the more heartbreakingly Pyrrhic.
In Batman: Going Sane by J.M. DeMatteis, a series of issues of Batman, Batman supposedly dies, and the Joker apparently becomes sane, got cosmetic surgery, and began calling himself Joseph Kerr. As soon as Batman recovered and appeared in public again, he reverted back to his villainous personality, and left the job and girlfriend he had gotten in the meantime behind without a second thought.
As he lay on his deathbed, Captain Marvel (not that one, the one that belongs to Marvel) had been disowned by his race, the Kree, as a traitor. But the Skrull, whom he had fought for most of his life, sent a representative to present him with a medal reserved solely for Worthy Opponents of the Skrull.
Augustus Caesar: "...What was it like, Lycius? In the days of the Republic? It was chaos, held at bay by a handful of men: Cicero, for example."
Lycius the Dwarf: "The lawyer? My father told me about him. He was a great man, wasn't he?" Augustus: "Yes. A fine mind, and an honorable man. The last of the giants." Lycius: "Cicero... whatever happened to him?" Augustus: "I had him killed." (Technically, Mark Anthony did, but perhaps Augustus felt responsible.)
In Invincible #100, the title hero is seemingly killed by Dinosaurus, his death broadcast around the globe because it happened during a really high-stakes superhuman fight. While it's revealed later that this was a clone created by Dinosaurus to fake Invincible's death, the world at large thinks him dead. Several of his enemies, including Kursk, Powerplex, and Titan, are seen to be disturbed and even upset by his death. The one most hurt by this development, however, is Angstrom Levy, his personal Arch-Enemy, because obviously Invincible being dead really puts a damper on his bitter revenge plot against Invincible. Thragg, the Viltrumite king, is the only one of his enemies shown to betray no emotion upon receiving the news.
In the Marvel ComicsThe Transformers series, Megatron becomes increasingly Ax-Crazy after the loss of Prime, attacking fellow Decepticons and going on enraged tangents and generally acting like he got swapped with cartoon Galvatron when no one was looking. In the end, Shockwave sends the Predacons to kill him so that he won't further endanger the 'Cons. Unfortunately, madness also doubles as Unstoppable Rage nicely.
Megamind is about the eponymous supervillain who defeats the hero, then discovers that even though he is finally victorious, without The Cape to oppose him the challenge is gone. The variation here is that the movie is about the supervillain, so he's technically not the antagonist.
Peter Pan has Captain Hook doing this when he believes the titular character died from the exploding gift he gave him.
Films — Live-Action
Given a nod in Kill Bill, when Bud and Elle think The Bride is dead. Bud asks Elle, who considered The Bride a personal rival/nemesis (in more ways than one), which R she feels: Relief, or Regret.
More importantly, Beatrix weeps in the bathroom after she succeeds in killing Bill.
Bill the Butcher in the movie Gangs of New York commemorated the death of his Worthy Opponent "Priest" Vallon every year with a public celebration. At one point, he laments that, of all the people he'd killed, Vallon was the only one worth remembering.
In Grumpy Old Men, the eponymous characters, John and Max, have been bitter antagonists for years. During the course of their biggest fight yet, John suffers a heart attack and nearly dies. A visibly shaken Max goes to see him in the hospital, and when the nurse asks if he's a relative, he replies, "He's my best friend."
In Kagemusha, when the death of Shingen Takeda is finally revealed, one of his rivals sings a song of mourning.
Lampshaded by M. Bison in Street Fighter after learning that Guile was seemingly killed in some random prison escape, claiming that he deserved the honor of going out with a broken spine at Bison's hands.
Nobody dies, but in the movie Spider-Man 2, Spidey hangs up (actually, throws out) the spandex. Jameson is just beginning to admit that the world is a darker place without him when the costume he had bought and pinned to his wall was swiftly abducted, changing his opinion mid-sentence.
In X-Men: The Last Stand, Magneto sincerely grieves over Xavier's death and cuts off his Dragon Pyro's irreverent talk about the deceased abruptly. As in most versions of X-Men, Xavier and Magneto were very close friends who eventually found themselves on separate sides due to their ideological differences.
Heathers has J.D. mourning over Veronica after she faked her suicide.
A temporary example in the first Artemis Fowl book when Holly mourns Artemis' "death".
Commander Root also displays a mild version of this when Mulch Diggums fakes his death.
In return, Mulch is horrified when Commander Root really does die at the hand of Opal Koboi.
In The Cardinal of the Kremlin by Tom Clancy, a Soviet general shows up at the eponymous character's funeral, despite the Cardinal being a traitor and American agent - but he was a national hero after all. While the general seems to accept the explanation and stays out of respect, he shows up without knowing the reason, only having been asked by the President of the United States, and as a person connected to the embassy, it would not do for him to decline.
Several times in Romance of the Three Kingdoms, Cao Cao is respectful of the soldiers he captures and cannot persuade to join his army, forcing him to execute them. He demands their loyalty be recognized and has them buried with full honors.
In The Book of Dreams, the last book of Jack Vance's The Demon Princes series, the last line is Gersen contemplating the fact that he has destroyed all five of the Princes, completing the vengeance he was raised from boyhood to achieve: "I have been deserted by my enemies. Treesong is dead. The affair is over. I am done."
Exit Music, the last Inspector Rebus novel (for now...?) by Ian Rankin. Rebus's arch-nemesis Big Ger Cafferty, the man who has been behind - or at least involved with - practically every criminal plot Rebus has ever investigated, suffers a heart attack at the end of the book. Rebus leaps on him, starts CPR, shouts for medical assistance, and quite disturbingly shouts "Don't die... don't let him die!!"
Frankenstein: When the creature realizes that Victor has died, he calls Victor the "select specimen of all that is worthy of love and admiration", despite having pursued the man to his end.
In the Alexandria Quartet, the cross-dressing old sailor Scobie is notorious among the Alexandria vice squad, who bust him with regularity. The burly squad members are last seen at his funeral, blubbering like babies.
In The Accursed Kings, after Mahaut of Artois is poisoned by her handmaid, her nephew and enemy Robert is pleased but not exactly overjoyed.
Inverted in the novelization of Batman Begins. Bruce built a sepulcher for Henri Ducard/Ra's al Ghul in his family cemetery next to Thomas Wayne after the event, and there's this exchange:
Bruce: "They both gave me my life. It seems fitting that they be buried together."
The Dukes Of Hazzard did an episode where Roscoe thought that Bo and Luke had drowned. Roscoe, who spent years as an enemy of the Duke family, was genuinely mourning them as much as their friends and family. The narrator had a line that summed up this trope, "Sometimes, losing an enemy can be like losing a friend."
Roscoe isn't really a bad guy though, he's a genuinely good lawman who's been duped and controlled by Boss Hogg.
Stephen: I'm conflicted here. Sure, I'm happy he's gone, [tearing up] but I have spent so much time hating him... that I think I love him.
Wiseguy. Music industry Big Bad Winston Newquay is genuinely upset over the death of his long-time rival Isaac Twine, though that doesn't stop Newquay carrying out his side of their bet to dance on the grave of the one who dies first.
In Star Trek: Deep Space Nine, Sisko has a deeply antagonistic relationship with Eddington, who betrayed the Federation. Sisko is utterly single-minded when hunting Eddington down. When Eddington and Sisko are in battle together, though, the wounded Eddington has to turn a gun on Sisko to convince him to leave him to die in battle. Sisko later acknowledges that Eddington was the most loyal man he knew.
The Trickster would probably mourn if the TV version of The Flash were killed, as evidenced by his scolding his female assistant when she even suggests killing the unconscious speedster. He even threatens her for trying to unmask the Flash, as his antagonistic fixation depends on the hero being some kind of god.
Ben Linus: [Delivering a eulogy] John Locke was a believer, he was a man of faith. He was a much better man than I will ever be, and I'm very sorry I murdered him.
Bonus funny points because none of the other characters were aware of that last bit beforehand. Cue some reactions of "wait, what?!?"
Frank Lapidus: (Burying the body) Weirdest damn funeral I've ever been to.
Locke's primary antagonist Jack didn't take his death very well either. In death Locke earned more respect from Jack and Ben than he ever did when he was alive.
In a period of the show before their relationship became friendlier, Police Captain Leland Stottlemeyer became upset in an episode of Monk when he thought the titular character was dead, despite not liking him very much. Humorously, he says "I loved that man", then finds out he's still alive, then says "I hate that man!"
In the Three Kingdoms 2010 TV version, of Romance of the Three Kingdoms, upon Zhuge Liang's death, Sima Yi is portrayed as saying the following words (translated from the original): "Now that you are gone, who else can know my mind as well as you did? Will I not be lonely?"
A variation on the "Protagonist in Mourning" angle occurs in Sanctuary. When Tesla is devamped, Helen is saddened by the apparent loss of all of The Five via death, de-powering, or just leaving her. This, even though non-vampire Tesla is a MUCH easier "foe" to deal with.
The Wire: Stringer Bell's death occurs just as the cops think they've cracked the case. McNulty is seriously dejected by this. "I had him. And he never even knew."
Doctor Who: After all prior and current incarnations of the Doctor are taken out of time in "The Five Doctors", the man the Third Doctor called his "best enemy" is called in to rescue him by the Time Lords. The Master agrees to try to reverse the complete elimination of multiple forms of his mortal enemy from the universe in part because of this trope.
The Master: A cosmos without The Doctor scarcely bears thinking about.
In October 1986, Dusty Rhodes and Magnum T.A. were scheduled to enter a steel cage against Ole Anderson and James J. Dillon. However, Magnum T.A. was involved in a horrific car accident earlier in the month, and would never wrestle again, leaving Rhodes alone in the cage against Anderson and Dillon. That is, until Nikita Koloff, well-known Russian heel and personal nemesis of both Rhodes and Magnum, entered the cage as Rhodes' partner. Koloff would dedicate that match, and several more after, to his fallen foe Magnum, making a Heel-Face Turn in the process.
Religion and Mythology
Older Than Feudalism: In The Bible, King David mourns for both Saul and Absalom, the former of whom tried to kill him before he became king and the latter who overthrew and exiled him. They were family, though (the former his father-in-law, the latter his son).
Done in the play Amadeus where Salieri is, for many years, Mozart's Unknown Rival and seeming friend, but works covertly to ruin his life. As Mozart continues to produce great works while losing everything, Salieri ironically ends up becoming the only person who realizes the full extent of Mozart's greatness and thus ultimately mourns him more than anyone else.
In Julius Caesar, after Brutus dies, Antony calls him "the noblest Roman of them all", and says that the others conspired against Caesar out of jealousy, but Brutus did it because he thought it was right. He and Octavian agree to give him a respectful burial.
While most productions do not portray him as a full-on antagonist, in Jesus Christ Superstar, Judas has a complete emotional breakdown after helping Jesus' arrest and execution, and commits suicide.
In Sonic Adventure 2, Dr. Robotnik utters a respectful farewell to Sonic after he thinks he's killed him.
Farewell, Sonic... My admirable adversary!
Shadow watches Sonic's "death", commenting, "I guess he was just a regular hedgehog after all..." in a slightly disappointed tone.
Also in Sonic the Hedgehog (2006), Dr. Robotnik, again, finds himself mourning the loss of Sonic, who was killed by Mephiles in order to make Elise cry.
In Tales of Vesperia, after helping to orchestrate a long chain of events that involves the death of Don Whitehorse, Yeager proves himself to be a Jerk with a Heart of Gold when he shows up in Dahngrest with a bouquet of flowers, indicating that while what he did was business, he personally regrets the loss very much and needs time to mourn before returning to his job. At least, that's what he says to the party.
On the online game Dragon Fable, Warlic is killed by his apprentice, Natherya. The people of Falconreach hold a funeral in front of a statue of him. Then, his greatest enemy Xan shows up, obviously angry over his death. However, Xan says that HE wanted to be the one to kill him, and is given the idea to bring him back to life just to kill him again. Do the math and guess how that turns out.
Happens in World of Warcraft when you kill Illidan. His last words to Maiev are "You have won... Maiev... But the huntress... is nothing... without the hunted... You... are nothing... without... me..." She agrees.
In Mafia: The City of Lost Heaven, Don Salieri is completely depressed after thinking that the main character had succeeded in killing his best friend and adviser, who had betrayed him after his wife and child were kidnapped (this follows a literary tradition of mobsters going to each other's funerals and providing for each other's families, even if they themselves had been responsible for the death). In truth, Tom (the main character) spared him after saving his family and setting right what his betrayal screwed up. Ironically, that didn't stop him from finding out he was still alive, having him killed for real, and putting out a hit on Tom for having spared him.
In Halo, even though they are now more allies than enemies, the Arbiter consistently says "Were it so easy" whenever someone makes a jab at killing Master Chief, or even on the rare occasion where he is killed by a Covenant or Flood enemy. He looks especially sad at the end of Halo 3
In Sengoku Basara: Samurai Heroes, Ieyasu and Mitsunari will mourn each other's deaths and cry openly (though for different reasons) in their red paths. Mitsunari in particular is at first first thrilled by his triumph, but soon realizes that his life has no meaning now that he's had his revenge.
One of the endings of Heavy Rain, "Ethan's Grave", can show the villain, the Origami Killer, hiding behind a tree, looking sad at the titular situation.
Roy Earle in L.A. Noire appears, giving a eulogy in the end at Cole Phelps' funeral, but he's faking it, making it a subversion.
Wings portrays the Allied forces as having a "bittersweet" reaction to the death of Manfred von Richtoffen. Truth in Television, as this really is how they reacted; see also the real-life section.
Gilgamesh Wulfenbach in Girl Genius spends several months in deep mourning when Agatha fakes her own death to escape capture by his father. While Gil never really saw himself as her enemy, his father, Baron Klaus Wulfenbach, has thought of her as a threat since he first realized that she was the missing Heterodyne heir, and the Baron only becomes more convinced when he learns that she can order the Other's minions and open portals in space-time. As Gil remains loyal to his father, and is also worried by the evidence that she may be the Other, he plans to capture her and verify that she isn't evil reincarnated before wooing her. Wooing her "Most Vigorously"!
Aku: "It would be a lie to say I do not miss the samurai. He may have been my greatest enemy but I also felt the most alive when he opposed me."
Neopets has an (Anti) Heroic example: after the death of longtime villain Hubrid Nox in "The Faeries' Ruin", the Advent Calendar featured an animation of Magax, visiting Nox's grave and holding a present he'd presumably bought before Nox's death.
Batman: The Animated Series: In "The Man Who Killed Batman" no-name goon Sid "The Squid" accidentally convinced many people, himself included, that he had killed Batman. The Joker was skeptical, but after holding up a jewelry store and just waiting there several hours to see if Batman would show up, Joker's skepticism and glee gradually vanished. In his usual bizarre way, Joker mourned the loss of his favorite adversary by holding a symbolic funeral for Batman inside the Joker's "birthplace", the Ace Chemical Plant, Harley playing "Amazing Grace" on a kazoo, locking Sid in a coffin, and dropping it into a big vat of acid, after which he fell a Single Tear for his lost adversary. Then, in typical Joker fashion, he bounces back afterward with a smile:
Batman, having survived the unintended explosion in the beginning of the episode, turned out to be watching from the shadows the whole time, waiting for his apparent demise to make a particularly troublesome crime boss careless.
When Superman was thought killed by the Toyman on Justice League, Lex Luthor appeared at his funeral. Despite the disgust of Lois, Luthor admitted to genuinely missing him.
In the unfinished Invader Zim episode "Mopiness of Doom," Dib gives up Paranormal Investigation to learn "real science" with his father. Zim finds himself too depressed to do any evil and winds up lying on the couch eating junk food. Dib is initially happy, but eventually realizes that he's bored and goes back to fighting Zim.
But somewhat pointedly Averted in "Bad, Bad Rubber Piggy". Zim manages to (temporarily) kill Dib (as a little kid!) and his response is...to quietly take a sip of his drink before merrily going on his way.
Dr. Drakken gives Kim Possible a brief eulogy when he thinks she's been shot by a laser cannon in "Graduation."
In the classic animated short "What's Opera, Doc?", a parody of Richard Wagner's works, Elmer Fudd as Siegfried hunts down Bugs Bunny in retaliation for the latter's disguising himself as Brunhilde. When he finally succeeds in his attempts to "kill da wabbit", he regrets it and tearfully carries Bugs away, cradled in his arms. Bugs revives for a moment to address the audience:
Bugs Bunny: Well, what did you expect in an opera? A happy ending?
This has almost always been Elmer's reaction when he mistakenly thinks he's actually killed Bugs, dating back to their first cartoon, "A Wild Hare." But "What's Opera, Doc?'' certainly plays it up the most.
Danny Phantom: Though he doesn't outright say it, Vlad Masters in a Bad Future blatantly admits his terrible actions resulted in the loss of those he was close to, mourning them for ten years strong—including Jack.
ReBoot: After Bob is gone, Hack and Slash realize that there is no one to stop them from finishing their evil acts anymore. This distresses them intensely.
In the Phineas and Ferb episode "Come Home Perry", Perry the Platypus was relocated to a new family and a new villain, and like everyone else who knew him, Doofenshmirtz was feeling a bit sad with the loss.
An inversion has Perry severely depressed and feeling betrayed after Doofenshmirtz gets a new nemesis and doesn't need him anymore.
Doofenshmirtz felt sad the one time he believed he had destroyed Perry.
Tom and Jerry Tales has the titular cat crying for the titular mouse, thinking he is killed by being crushed by a pillar. Afterwards, Tom gets haunted by Jerry's "ghost", not knowing that the mouse is alive and that he and his bat-lookalike are trying to scare him.
One of the original Tom and Jerry cartoons, "The Lonesome Mouse", has Jerry celebrating that Tom has been kicked out of the house. Before long, though, he finds that life without Tom is boring, so he conspires to get him back.
In the episode "Emperor Joker", when The Joker obtains God-like powers, he finally defeats Batman. Though seemingly saddened by the loss of his adversary, it's immediately subverted when he laughs it off and resurrects him to do it again and again.
The Joker: "I can't believe it. He's...he's actually gone. Let's take a moment to reflect on the passing of a man who was more than just another do-gooder in tights! He was the best archnemesis a sociopath could ask for! Okay! Lets do it again!"
Averted in the book. Hook dies and everyone goes home, but when Peter Pan returns to Wendy he has no memory of Hook... and indicates he has a long string of villains that he forgets after they die. Creepy.
In a non-death example from The Simpsons, Bart gets Principal Skinner fired and soon realizes that he misses him as an enemy (the new principal is Ned Flanders, who is too nice to curb any kind of misbehavior). Lisa mentions the trope, explaining that Moriarty needs his Sherlock.
In a later episode, Flanders moves away to be replaced by a new bully neighbor who causes Homer to miss Flanders and attempts to get him back.
The South Park episode "Smug Alert" shows Cartman at first rejoicing the fact that Kyle along with his family has moved to San Francisco. But since Butters doesn't really cut it as a Jewish nemesis to him, Cartman decides to brave lethal clouds of "smug" (emitted by people who drive hybrids) to save and bring Kyle back to South Park (in secret, of course).
Cartman: We just can't get rid of you, can we, sneaky jew rat!
Kyle: Don't belittle my people, you fucking fatass! (Leaves)
Cartman: Ah, that's better.
Uesugi Kenshin reportedly cried at the death of his greatest opponent, Takeda Shingen, with whom he had previously fought a lengthy series of battles.
Fidel Castro felt this way about President Kennedy; when asked about his assassination, Castro said, "What I felt when I heard that news is someone who has an adversary, someone who respects his adversary and all of a sudden, someone else kills his adversary. A boxer in the ring for example, and the adversary is shot to death in the middle of the boxing match."
Manfred von Richthofen was regarded with the greatest respect by most Allied airmen. When he was eventually shot down and killed in 1918, his aircraft crashed behind allied lines in a sector controlled by the Australian Imperial Force, and he was given a funeral with full military honours by No. 3 Squadron, Australian Flying Corps.
Julius Caesar wept at the death of his friend turned rival Pompey, after being presented with his severed head and hand by the Egyptians after Pompey tried to seek sanctuary with them. Some of this might have been for good P.R., but he might have also genuinely believed that Pompey deserved a far more dignified end.
Caesar had the killers put to death, for the above reasons and also to make the point that foreigners did not get away with assassinating Roman officials.
Plutarch writes that Octavian wept when a member of Mark Antony's bodyguard brought Antony's sword to him. It was almost certainly not because of any lasting affection for him, but by that time, they had been fighting on and off for fourteen years. Octavian had crushed every single one of his enemies at last. The feeling of so many years of conflict finally being brought to a close probably made him pretty emotional.
The last chapter ("666") of Hunter S. Thompson's Better Than Sex is a meditation on the death of Richard Nixon. He starts by saying that it was Nixon (or rather, his dislike of Nixon) that got him into politics, and "now that he's gone, I feel lonely"... and then ultimately subverts the trope by eviscerating the late president, writing a vitriolic screed that finishes by saying that Nixon "killed the heart of the American dream."
Erwin Rommel received a moving tribute from Churchill upon his death; it was still the middle of WWII at the time.
During the North African campaign, Rommel ordered that British Major Geoffrey Keyes, the commander of the failed British attempt to assassinate him, to be buried with full military honors. Not only was Keyes killed during an attempt to kill Rommel, Rommel was under orders to treat British commandos as spies, not as soldiers at the time.
Formula One champions Alain Prost and Ayrton Senna were bitter rivals throughout their careers, even crashing into each other at times to screw each other over. Prost even had a clause in one contract that Senna could not be his teammate, the rivalry was so strong. When Prost retired the second time, they tried to repair their relationship, but sadly Senna died a few months later during the Blackest Weekend. Prost, as it turns out, was one of his pallbearers.
To this day Prost is reluctant to talk about Senna, and admits a part of himself died that weekend as well.
After the death of Pitt the Younger, his great political rival Charles James Fox said "It feels as if something is missing in the world."
Frederick The Great upon the death of Maria Theresa: "I have shed some very sincere tears at her death. She has done honor to her sex and to the throne. I have made war upon her, but I have never been her enemy."
When 17th century Dutch admiral Michiel de Ruyter died a week after being injured during a navy battle with the French, the French king Louis XIV fired canons as a salut when the ship carrying the body of Michiel de Ruyter sailed by.
After the Battle of Trafalgar, the British respected the Spanish admiral Cosme de Churruca so much that, having captured his ship, they placed a brass plaque on the door of the cabin that had been his, and all who entered it were required to remove their hats in salute to a very Worthy Opponent.
Pierre Trudeau's funeral provided a twist on the trope: not because old rivals and political opponents paid him tribute and mourned the passing of one of the most charismatic leaders the country has ever had, but because it was an example of Antagonists in Mourning for someone else. The funeral was attended by both former US president Jimmy Carter and long-time American enemy Fidel Castro, who sat beside one another and were both Honorary Pallbearers.
Political differences eventually cropped up among the leaders of the movement that became the Meiji Restoration in 19th-century Japan, but that didn't always make things bitter. Yamagata Aritomo is notably said to have wept over the severed head of Saigo Takamori, his former comrade who'd led the only rebellion against his regime worth mentioning.
Carlton Fisk broke down in tears when he found out Thurman Munson was killed in a plane crash.
Similarly, Joe Girardi choked back tears in announcing the cancellation of a game due to the death of rival pitcher Darryl Kile.
From the book Blind Man's Bluff, when an American and Soviet submarine had a severe collision in the ocean, and both believed the other had died, the sailors on both submarines felt genuine regret at the death of fellow sailors, even though they were opponents.
When one of the most famous historical figures of Argentina, Juan Domingo Perón, died in 1974, the most touching words of mourning came form his political antagonist, Ricardo Balbín: "This old adversary farewells a friend".
After Janos Hunyadi's death, Sultan Mehmed II said: "Although he was my enemy I feel grief over his death, because the world has never seen such a man."
A rare case in college baseball: When the University of California's baseball team was threatened with disbandment after budget cuts, fundraisers were held to save the team. Among the donors was Cal's biggest rival, Stanford University, whose fans made plenty of donations. According to former Cal baseball player Doug Nickle: "I don't think Stanford has any problem if Cal loses, but I think they had a problem if Cal didn't exist."
In the Scottish Premier League nearly every season has been a battle between the "Old Firm", Glasgow based clubs Celtic and Rangers. However in 2012 Rangers found themselves relegated to the lowly third division due to going into liquidation. Whilst Celtic were of course quite happy to mock their bitter rivals with their impending doom looming, many players and fans have admitted it just isn't the same without their nemesis around. Especially considering their clashes on the pitch were the highlights of any given season. Though it's likely only a matter of time before Rangers make their way back to the top division.
In the story of the Forty Seven Ronin, the lead of the titular group, Ōishi, pretended to be a hopeless drunk in order to escape the attention of his enemies. During this time, he was attacked by a random passerby who accused him of being a coward for not seeking revenge for the death of his master. After Ōishi and his men exacted vengeance on their enemy and committed seppuku, the same passerby, now ashamed for what he had done, visited the graves of the ronin and committed suicide. His body was then buried alongside theirs.