Often times the Commander, being as such, had access to better armor (he may be the only one outside his honor guard to have any, depending on the historical moment), so they were the ones that were harder to kill off.
The idea of a decapitation strike in nuclear warfare essentially involves the destruction of targets which are known to be the location of individuals with launch authority to their own nuclear warheads. The idea only really became feasible when delivery systems with very low warning times (such as submarine-launched missiles) or observability (such as stealth bombers) became available. It didn't last long for two reasons: first, a number of responses (such as devolving launch authority when senior leadership was unreachable) were implemented in response. Second, numerous potential problems were identified with an approach like the enemy managing to order a launch before they could be destroyed or a "headless chicken" scenarionote (professional military strategists prefer the term "spasm war") where a country just lashes out with nuclear weapons at every possible suspect in a chaotic fashion. Russia even created a special emergency control device to facilitate this "headless chicken" launch, known as the Perimetr (a.k.a. the Dead Hand).
Modern command ships are designed/ retrofitted to be fairly durable, stealthy and fast so they can avoid this trope. Most designs feature no real offensive armament but incorporate excellent point defenses.
Warfare
This was a frequent strategy of Alexander the Great. He would hold his personal forces and bodyguards in reserve until an opening appeared wherein he could go straight in and kill the enemy general. He used this quite effectively against the Persians, scaring Emperor Darius III into fleeing the field in Gaugamela. This was often necessitated by his substantial numerical inferiority, as no matter how brilliant his tactics, he knew that sooner or later the much larger enemy forces would wear his men down unless he could take out the enemies' commander.
Bonus points to Alexander for invoking anddefying the trope at the same time and in the same battle with his famous Rousing Speech at Gaugamela: different authors gave different versions, but the gist of it was, "should you kill the Persian High King, we would win the battle; should they kill me, we'd just have one less lance in this battle". Ironically, judging by the Macedonian Succession Wars, he might have not been exactly correct.
According to historical records from the Three Kingdoms – Shu, Wei, Wu period, a Wu general named Ding Feng was famous for this. His standard tactic in battle was to identify the enemy general that was holding the enemy's banner, then charge right for that general and kill him. He managed to survive doing this several times and was rapidly promoted to being one of the most powerful and prominent generals in the kingdom.
In the legendary last battle of El Cid Campeador (historians are more or less sure it never happened, but it makes a good story), this was the fear of his wife as she prepped the corpse so the soldiers wouldn't lose morale by learning that their commander was down. This made him Trope Namer for the El Cid Ploy.
Battle of Las Navas de Tolosa, 1212. The Christian forces were half the Muslim's. Instead of engaging them directly, the Christians took a long detour through a mountain passage they had just discovered and went straight for the tent of the Almohad Caliph, which was guarded by chained Slave Mooks. The Caliph escaped, but his massive army was rooted out and the Almohad empire in Spain essentially destroyed.
Averted in the fall of Constantinople when the Last Emperor of Rome tore the imperial insignia from his armour and charged forward (at the enemy who outnumbered them by more than 12:1 overall) with his men, making this trope impossible.
The French attempting this strategy is the reason why they lost the Battle of Agincourt. So many knights tried to capture Henry V (mainly because they were hoping for a literal king's ransom) that they got in each other's way, resulting in the entire cavalry charge being one big easy target for the English archers, after which the unhorsed knights got bogged down in the thick, sucking mud, many of whom then got trampled to death by the knights who hadn't been unhorsed yet.
King Richard III attempted this at the Battle of Bosworth Field. With the battle starting to tip against him, Richard spotted Henry Tudor and his party riding off towards the army of Lord Stanley, which at this point of the battle was hanging off to the side, neutral. Richard took the men around him and went after Henry. Henry's bodyguards fought Richard's men off, Stanley's army finally interceded on behalf of Henry Tudor, and Richard was cornered and killed. Tudor became King Henry VII.
From the Wars of the Roses: the First Battle of St. Albans was a battle between armies of thousands, but ended as a decisive Yorkist victory when the Duke of York's men went straight for the Duke of Somerset and killed him. The total number of casualties was less than 100.
Before the Battle of Pavia, the forces of King Charles V commanded by his lieutenants Charles of Lannoy and Fernando de Ávalos had been trying to find the best way to break the French siege of Pavia, of which King Francis I of France himself was acting as commander in chief. Ultimately, deciding to invoke this trope in a night raid, Ávalos and company quietly pierced the wall that surrounded the French camp and infiltrated in a multi-pronged attack with the goal to capture Francis. Although ironically they couldn't find Francis because he wasn't where they had calculated, the attack was devastating enough that the French army was thrown into chaos, provoking Francis into leading a reckless charge against the enemy cavalry that got him finally captured. With this victory, the entire war ended, although another similar war would explode years later when Francis was freed.
Another textbook example is probably the Battle of Otumba (1520) during the Spanish Conquest of the Aztec Empire. The Spanish and Tlaxcaltec survivors of the Noche Triste, led by Hernán Cortés, were retreating back to Tlaxcala when they were cornered by an Aztec army that, according to the lowest estimates, outnumbered them 10 to 1. The Cortesians had lost their cannons in Tenochtitlan and had little gunpowder and only 13 horses left. However, Cortés knew from previous battles that if he killed the Aztec commander, the Aztecs would withdraw until they could either receive or choose a new commander, as that was how battles were decided in Mesoamerica. He therefore led a cavalry charge through the Aztec lines, and one of his soldiers, Juan de Salamanca, managed to kill the commander and capture his standard and feathered helmet. The fact that this was the first cavalry charge ever seen by the Aztecs contributed to Cortés' victory: up to that point, as the Spanish had used their horses in front of them only as pack animals and to celebrate parades and games, the Aztecs had at best a very vague idea of how they could be used in war, so when the charge happened, their shock was multiplied. The success allowed the Spanish and their allies to retire to Tlaxcala, where they rebuilt their forces with other natives factions before attacking Tenochtitlan again the next year. Right around the same time, the Aztecs were being decimated by smallpoxnote Really the other way around, instead of 1 in 10 being killed (which is what "decimate" actually means) it was more like only 1 in 10 survived timely caused by a Spanish slave lost during the Noche.
Deliberately invoked at the Battle of Lepanto, where both flagships fired a single cannon shot before the clash to reveal their position to their enemy; the two flagships then locked bows for a vicious seesaw fight as more and more galleys piled onto the melee in the center. Despite nearly being overrun during the battle, John of Austria led his men to storm the Ottoman flagship, where Ali Pasha was killed, his head raised on a pike, and the banner of the Holy League raised over his flagship, thus breaking the morale of the Ottoman center.
Similarly failed to work with Admiral Yi Sun-sin in the Battle of Noryang. His Korean fleet and Chinese allies were routing the Japanese fleet that outnumbered them around 3 to 1 when Yi was struck by a stray bullet. Well aware of his trope, the dying Yi's final order was to conceal his death and maintain the pursuit. His son and nephew quickly pulled him into his cabin before the rest of his flagship's crew could notice, and the latter put on Yi's armor and returned to the deck, loudly beating the war drum so it would look like the admiral was still in command.
During The Eighty Years' War, the Spanish imperial army led by Fernando Álvarez de Toledo, Duke of Alba, besieged the city of Mons (no, it was not a city of Mons, sadly) and awaited for the Dutch-English-French rebel forces led by William of Orange to come to relief it, especially given that the siege had trapped William's own brother Louis in the city. After the relief attempt was repulsed, Alba then ordered a surprise raid by Julián Romero in the Dutch camp to capture William himself. In a subversion, though, the latter managed to flee at the last second thanks to being alerted of the attack by his Spaniel dog.
During the American Revolution, particularly at the Battle of Saratoga, colonial sharpshooters would specifically target British Officers knowing it would render their subordinate formations ineffective. Many of the German and British military leaders considered this to be in very bad taste as Napoleonic warfare on the European continent at that time period highly discouraged such tactics.
Notably failed to work with Admiral Horatio Nelson during the battle of Trafalgar, as the English fleet went on to destroy the French even after his critical injuries.
This was how Texas won its independence from Mexico. After defeating a numerically superior Mexican force at San Jacinto in a sneak-attack Curb-Stomp Battle, the Texans found and captured the Mexican general Antonio López de Santa Anna the next day, after having tried and failed to retreat. The Texan commanders forced Santa Anna to sign the Treaties of Velasco establishing the independence of the Republic of Texas — much to the chagrin of Mexico's infuriated leadership, who saw the treaties as having been signed under duress and would continue to lay claim to Texas (either in whole or in part) until the Mexican-American War.
The reason that British infantry officers stopped wearing swords in World War I was not so much because the swords weren't useful, but rather because German snipers could identify an officer by him wearing or waving around a sword, and shoot him first. The cavalry didn't have this problem because all of the troopers used swords, not just the officers.
During World War II, the allies initially wanted to assassinate Adolf Hitler to end the war. Then they realized that doing so would allow a better commander to take his placeand only make things worse, since Hitler was a poor military commander. They did successfully assassinate Reinhard Heydrich in 1942, as he was considered far too dangerous and far too efficient at managing occupied territories for the benefit of the German war machine. The way the Nazis reacted to that, however, ultimately led to further assassination attempts being called off. Still, independent of what the Allies thought, various people tried to kill Hitler — they just all failed, giving Hitler (who believed himself to be chosen by destiny) an even bigger chip on his shoulder.
In the Pacific Theatre, Japanese officers were often picked off with ease by snipers. After all, they only had to look for the guy who had a conspicuous scabbard by his hip, as swords don't make for very good concealable weapons. For the Japanese, the sword was not only part of the officer's uniform but something they actively used in combat, so they would never give it up even if it was highly conspicuous.
In 1943 U.S. military intelligence intercepted a message stating that Admiral Isoroku Yamamoto, commander of the Imperial Japanese Navy, would be flying from point A to point B at a certain time. The Americans successfully intercepted the plane and shot it down, killing Yamamoto, the architect of the attack on Pearl Harbor.
The attempts of the CIA to assassinate Fidel Castro were legion. Whether all of them actually occurred is anybody's guess, but due to their sheer number, some of them must've been real. Castro of course died peacefully after retiring from decades of power, having outlived many of his would-be assassins. Castro once told Vladimir Putin that the only reason he was still alive was because he personally managed his security detail instead of letting some State Sec official do it for him.
The story goes that after one too many assassination attempts against him ostensibly ordered by Moscow, Josip Broz Tito sent back a letter to the effect "Stop or we will send one, and we'll only have to send one". It worked.
In modern times, concern about snipers using this very tactic has led to the phasing out of identifying marks for officers, with inconspicuous rank insignia, and salutes by soldiers of lower rank expressly discouraged. So, Bling of War is now no longer worn on frontlines, only in safe and peaceful places. Medics have had the same problem, even though shooting them is generally a war crime (of course, in today's wars, often one side or another doesn't care about the laws of war — hence the problem).
Politics
In a Parliamentary political system in which people holding an executive office must be elected to Parliament through the standard MP electoral process, this kind of thing is often talked about. Despite most party leaders holding a safe seat (and it being fairly easy to shuffle a party leader to a safer seat if you are a bit worried), any election that they are defending will inevitably see a disproportionate amount of minor and joke candidates join in, and in rare cases other parties may even make attempting to dethrone them part of their electoral strategy. The actual merits of doing this is often debated, as it is often pointed out that if a high-profile politician is at-risk of losing their seat in an election, the rest of their party typically isn't doing well either, and you would be better served running a broader campaign rather than chasing the headline win.
A good example of this is in the United Kingdom 2015 General Election, in which the Labour Party dedicated a large amount of resources and grassroots activism to trying to win the seat of Liberal Democrat leader and Vice Prime Minister Nick Clegg. They were successful at this, and the moment became a useful shorthand for the loss of the Liberal Democrat's fortunes during their time in the coalition government, but in the broader picture this win likely came at the expense of winning many more Conservative-held seats in the north that had far smaller margins, and which were ultimately more consequential for the election's overall outcome.
Sports
In American Football, this is basically the whole idea behind the 'sack', with the commander being the quarterback.
in a sneak-attack Curb-Stomp Battle, the Texans found and captured the Mexican general Antonio López de Santa Anna the next day, after having tried and failed to retreat. The Texan commanders forced Santa Anna to sign the Treaties of Velasco