In The Legend of Zelda: A Link to the Past, the Master Sword can be upgraded twice, making the original Master Sword your Infinity Minus Two Sword. Which is funny, considering there are only 4 swords in that game. Infinity Minus Three would be your starting weapon.
Also in The Legend of Zelda: Ocarina of Time the Master Sword is overpassed in range and damage produced by the Biggoron Sword. Its obtained in an optional quest and only has the disadvantage of needing to be wielded with the two hands making it impossible to use the shield. Still, the weapon used to finish the Big Bad is the Master Sword. The Biggoron Sword will work for most of the fight, but only the Master Sword can strike the finishing blow.
To make the Crissaegrim even more game-breaking, it's possible for two of them to be dropped. Since they're one-handed, you can dual wield them.
Additionally, all other primary weapons in the game require you to stop in place to swing them. The Crissaegrim has no such restriction, allowing you to continuously swing it while running.
First Person Shooter
This can happen in Borderlands with Atlas guns. They're supposedly the best you can get, but due to the random weapon generation system, it's easily possible to get much better guns from the (allegedly) worse brands like Tediore and Vladof, sometimes even from the exact same loot source.
The BMW M3 in Need for Speed Most Wanted definitely counts. You can get much better results from a fully tuned Vauxhall Monaro by the time you recover it.
I see your Vauxhall and raise you the Fiat Punto and Cobalt SS, which are tied for 3rd fastest cars in the game after the Carrera GT and Lotus Elise given full junkman parts. That Cobalt just keeps accelerating.
Honestly, one of the coolest parts of the game is the fact that you can take a Golf GTI and make it faster then the police spawning engine at level 5 is sweet
Only in single player. In multiplayer, its stats are so utterly sad that the game takes mercy on you and detunes the other cars. Unfortunately, it does so by lowering their handling while buffing the handling of the M3... which neatly solves its biggest problem and transfers it to everyone else. If there is so much as 1 M3 in a multiplayer match, you have to roll out your own because any other car will now drive on ice.
The boss cars in Need for Speed Pro Street are nearly useless. For beating the Grip King, you get an M3. Yay. You're probably driving at least a 911 Turbo if not a Pagani Zonda at that point. The Speed King's GTO is one of the slowest cars in the game, not to mention its complete lack of downforce which prevents you from even going fast at all without randomly flipping over and exploding into pieces. And even discounting the many glitches in drag that allow you to build a 3.5 second Toyota Supra, the Mustang you get from the Drag King is probably worse than any other RWD car you can buy except the Aston Martin. And the ultimate end boss car is a Lancer Evo. The only sensible boss car is the Drift King's RX 7.
Expect to do a lot of grinding if you want the Ultimate Weapon for your favorite character in Dissidia: Final Fantasy (and yes, it's different for all 22 of them)... but turns out that the actual Ultima Weapon is a huge case of Guide Dang It requiring special passwords, materials, and Item Crafting recipes to create. And even then, it is a Situational Sword which is only at its best when you have max HP.
In the Soul Calibur games, characters who get Soul Edge, supposedly the most awesome sword ever (except to people who know about the Soul Calibur), have a Legendary weapon that trumps Soul Edge.
This varies, however, depending on the particular stats and effects of each characters particular Soul Edge and Legendary Weapon.
Strangely, the Kingdom of Loathing has three. At about level five, you get to smith your class's "Epic Weapon", which has a high power, gives a large stat boost and (for some classes) doubles the duration of buffs that they cast. Soon after that, you get to turn it into the "Legendary Epic Weapon", which has even more power, a larger stat boost and triples buff duration. During the final part of the Nemesis Quest, the LEW upgrades to the Ultimate Legendary Epic Weapon when fighting your nemesis's One-Winged Angel form. The ULEW all have the highest possible weapon power (coupled with a lower-than-normal requirement to equip), large stat boosts, all the benefits of the older forms and give access to a special combat move when equipped - and for buffing classes, the buff duration is quadrupled.
Then, when it all comes down to it, it doesn't match up to half the weapons you find later on.
Any ultimate weapon in World of Warcraft that's from an earlier expansion pack (or, goodness forbid, from the unexpanded game). Thunderfury, for example.
Really any gear from previous content. Within the same expansions the best gear from one raid tier (with some exceptions) lies between the low and medium grades of the next tier. When new expansions come out, the very best and hard to get stuff from previous one is eclipsed by lowly quest rewards before long. More, Cataclysm has made it so that it's finally true what people have been incorrectly (exaggeratedly) claiming about the previous expansions: the lowest new items are immediately a match (almost) for the best old ones. It's probably because getting really good stuff was made much easier in the previous expansion.
Happens a lot in Maplestory. Considering the max level being lv 200 and the highest level equipment available overseas in the (original and content-heavier) Korean version being 140, there will always be much room for game designers to add better, and stronger equipment in the future.
Not only do new equipment could come out, new, more dependable methods of improving existing equipment have come out often over time. Any weapon considered good before new items used to enhance equipment come out, would be less good because it becomes easier (though usually either more risky or costly) to make something better then before.
Role Playing Game
The Excalibur from Final Fantasy I is second in power to the Masamune, which is found in the final dungeon. Odds are good, though, that you'll let the Fighter/Knight keep using Excalibur - it can only be used by Fighters/Knights, while the Masamune can be used by anyone, so you'll probably give it to your Thief/Ninja or Red Mage/Red Wizard.
In the Dawn of Souls release for the Game Boy Advance, you obtain the Ragnarok after defeating Shinyru on the 20th level of Lifespring Grotto. However, after you complete all 40 levels of Whisperwind Cove and kill the weaker Death Gaze and obtain the less powerful Lightbringer, you can find a treasure chest that contains the Ultima Weapon, a sword that does damage based on the wielder's HP, making it twice as strong as the Ragnarok.
The 20th Anniversary Edition tops this with the Barbarian Sword, which has 134 attack, where the Ultima Weapon could only go up to 100.
While you spend at least one-third of Final Fantasy II chasing after the Ultima spell, it really isn't that great if the player doesn't max out every spell, weapon level and stat; otherwise a Flare or Holy spell does more damage.
Tales of Symphonia: Lloyd's Material Blade is outclassed quickly by the Ninja Sword found in the last dungeon (to add insult to to injury, the Final Boss is also weak to it) and two sidequest rewards (the Valkyrie Saber and the Kusanagi). Lloyd's Devil Arm should outclass all of them unless you have been running from most of the fights. Even sadder, the paper fans you can buy in Luin are at least as good as, if not better than, the Material Blade. Funnily enough, the scene where Lloyd gets the Material Blade is accompanied by this quote: "I doubt you have a blade in your possession that can match it." Guess what? You can get one of these sword sets before that point.
In Eternia, the Eternal Sword might also still count depending on when you get it. As it was only the ultimate weapon in terms of sheer power, sacrificing other stats for it. Not to mention its Time element weakens it against certain enemies. The game had a few other weapons like it too. The true Infinity+1 Sword was the Last Fencer. While not as strong in terms of sheer strength, it had no element, and the advantage of raising all stats at once. It also may or may not be named after one of titles Cless gets in Tales Of Phantasia. So um... Take That?
Although the Dragon Sword is implied to be the Infinity+1 Sword of the first Breath of Fire, it is outclassed by not only the Trirang and the Emperor's Sword, but one weapon you can buy from a store, the Flame Sword.
The Ultimate Bat in Earthbound is an Infinity Minus Four Weapon; there are actually four more bats in the game with greater offensive power, three of which are discovered in the course of normal gameplay. The Legendary Bat is quite strong, but the super-rare Gutsy Bat is the true Infinity+1 Sword, not because of its raw power but its higher Critical Hit chance.
In Star Ocean 2, Claude's Penultimate weapon is the Eternal Sphere, which stuns enemies with each blow. It's very much out-classed by the Levantine found in the final dungeon, with nearly twice the attack power.
That depends on if you have an angel armband equip or not. For almost all the games fights the eternal sphere is the best because all competition is obtained nearly after the main story is finished and every attack you do throws out 12 stars that stun the enemy and do half the damage of your standard attack. Once you equip an angel armband though the eternal sphere loses its edge over better swords because every attack does this regardless of the weapon and you get some rather hefty stat boosts plus all element immunity. Of course this awesome item can only be obtained if you manage to beat one of the hardest bonus bosses in the game.
Sword of Vermilion is a repeated offender. The titular sword is not the strongest sword in the game, there is a stronger blade in an obscure dungeon. It's not even a Sword of Plot Advancement, getting it is optional and it can be missed. (Especially by Save Scumming, as getting it requires you let something bad happen to your character.) Also, the game features two items called Ultimate Sword and Ultimate Armor. Neither of them is. And the Dragon Shield, which is heralded as very powerful and requires a little backtracking to get, still isn't as powerful as a shield you can simply buy in the very next town - but at least you get the Dragon Shield for free.
In Chrono Trigger Masamune doesn't remain Frog's best weapon for long. (But much later, its upgraded version does.)
Which is all but worthless except as a Bragging Rights Reward, because the Vorlik can hit the damage cap anyways.
The original Ys plays this absolutely and irredeemably straight, forcing you to collect the legendary silver (!) equipment before you enter the final dungeon, then giving you better equipment of each type if you search the right treasure chests in that dungeon. Ultimately, the stuff isn't even necessary for beating the final boss, apart from the previous But Thou Must.
Actually, using the better equipment you gain in the final dungeon makes the final bossfight significantly harder.
In fact, in many of the games, the final boss can only be damaged with the penultimate sword.
In Tactics Ogre, the Penultimate Weapon is the Brynhildr, which drives much of the plot and plays a vital role in the final dungeon. However, it's outclassed by multiple weapons in the PSP remake.
In Lufia II the Sky Sword you can find in the Ancient Cave and the Dragon Blade you can buy for an insane amount of money in the casino are stronger than the legendary Dual Blade.
While not exactly weapons, this trope can apply to certain mons in the Pokémon franchise due to their extremely flattering Dex entries. The legendary Regigigas, for example, was said to have moved entire continents by pulling on them with a (very durable) rope. Rampardos, a prehistoric but otherwise unremarkable 'mon, just so happens to have slightly higher attack power. Even Arceus, the Olympus Mon that reputedly created the Universe, only has a base stat of 120 for each of its statistics. While this gives it the highest base stat total in the series, this does mean a fair number of legendaries and Com Mons are individually faster, stronger, or more durable than the creator god.
Arcanum's "Quench Life" spell, described in-game as One-Hit Kill against any living creature. Some creatures just need to be one-hit killed multiple times before grasping the principle of death.
Shadow Hearts: All the games have a penultimate weapon (The first game even had penultimate armor) available in the last two dungeons, usually in chests and some obtained in the trials. These weapons can't be found anywhere else, so once you sell them, they're Lost Forever. Some of the trials require less damage done to win, so these are worth holding onto. Karin in Covenant actually gets two, one got at the end of Disc One, and the other found in the penultimate dungeon. The real ultimate weapons are usually found in side quests.
The Silver Sword of the Gith is unquestionably the most powerful weapon in Neverwinter Nights 2, but this doesn't make it good — it's untyped, has stat bonuses for every stat (but middle-level at that), and offers a variety of narrow benefits. Monks especially find it frustrating — while it gives a bonus to unarmed combat, it has to be equipped for this, so the monk is now armed. On top of that by the time it reappears in the Mask of the Betrayer expansion the system is set up to let you make a weapon that's probably better out of random junk.
Out of all the weapons like axes, knives, bats, crowbars, and even gunsfound throughout Silent Hill: Downpour, the one you want to hang onto is the Fire Hook. It has the highest range out of all melee weapons, is unbreakable, only incapacitates enemies (not killing enemies is mandatory for the best ending), and has the secondary purpose of reaching fire escapes. It even beats out the weapons found in the green lockers.