Minecraft has a pretty solid vanilla experience but the depth of things you can do with mods is pretty insane. I’m playing a pack right now that basically turns it into a rogue like dungeon crawler.
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Definitely Minecraft, you can turn it into a completely different game
Tabletop Simulator and Garry's mod is all modding, they would be very boring without it. (Tabletop might have the DLC addon content worth playing).
Cities Skylines fixes many of the broken aspects of vanilla and adds things to the point that Paradox added some of them into an enhanced console edition.
Slay the Spire, it's already an amazing game to begin with, but mods allow it to be absolutely insane with customization and cards. Even multiplayer is supported (Together in Spire) and works quite well!
American/Euro Truck Sim has a multitude of mods that add great stuff and even more realism to the game.
Call of Duty Black Ops 3 is more or less a bog-standard shooting game without mods, but the number of crazy, funny and innovative maps for zombies gives it an insane amount of replayability.
Rimworld. The Vanilla Expanded mods alone have more content than the base game + all the DLCs
Definitely RimWorld. There's so many mods that improve the base game. From QoL mods that make you wonder why that isn't default in the vanilla game, to mods that complety overhaul the actual win condition. Just overall a really fun, replayability, frustrating game.
Use mods though. It'll make it better. Check out p-music mod while you're at it.
Late to this post but to me it's Minecraft. It has such an insane amount of replayability and can be turned into a totally different game depending on the mods and whatnot.
Another vote for RimWorld, though I want to point out that the game is perfectly playable without mods, too. It is not uncommon to see someone with hundreds of mods, but the vanilla game is just as fun. People have logged thousands of hours without mods.
Factorio all the way. Get bored of finishing the game, or crafting the perfect megabases? Prepare for mods that can take 1000s of hours to finish. Perfection.
As always, the factory must grow.
I know it's not as rich or developed as the Fallout or Skyrim franchise, but my fun little time waste Stardew Valley is greatly enhanced by mods.
The base game is incredibly fun and simple, but even the most basic mods enhance the "quality of life", making some of the more surface time eating elements easier. But then you have entire new world maps, NPC's, quests and full DLC-esque mods such as STV Expanded almost a must-have for long term players.
As an FYI, I'd highly recommend the game to even the most hardcore gaming aficionados. It's refreshingly amusing and low-key, so when Elden Ring has you ready to throw your controller at the TV, it's a nice mental break.
Plus the guy that created it learned how from scratch and coded the whole thing solo- the source, the sprites, even the music. And every upgrade and addition he's made over the years, easily 2-3 DLC's themselves, he's given away for free. Support indie devs!
There are plenty of older games where running some kind of widescreen or compatibility mod to get it working on newer hardware is the only way to get it running well, but that's kind of a boring techie answer.
In the spirit of the question, I'd say Fallout 4. The base game has a story I don't care about, factions that make no sense, and very little in the feeling of actual threat. I usually run between 200 and 300 mods to turn it into a truly post apocalyptic hellscape with functional radiation storms, low visibility in dust storms, darker night, less HUD clutter, more ghouls, proper flashlights, retuned weapon damage so things aren't so spongy, lots of new gear and weapons (I add in real guns but try to be tasteful and not add too much super modern tacticool stuff, but more cold war and vintage guns), backpacks, re-dress the Minutemen so they don't look like 1776 LARPers. Add tons of new sidequests and stories to find. The world becomes, this amazing, terrifying place to just explore and forget about the main plot. Returning home to my concrete walled safe settlement and my personal bunker living space really feels earned after exploring.
Similar to FO4, I feel the same way about Skyrim. Vanilla it's fine, but the graphics and interface QOL mods make a huge difference.
The original Doom for sure. I don't know if they count as mods since they're technically running on a modified version of the engine, but there is still a massive community making maps, mods, and even new game modes for it. Most recently the "MyHouse.wad" map for it has exploded in popularity. I've had so much fun over the years with doom mods, it's a treasure trove that most people have no idea exists.
There's even entire new games built on Doom. Sonic Robo Blast 2 Kart (stupid name, I know) is a fantastic free open source karting game with a decent community, and it's technically just a doom mod.
If anyone here is going to play a single doom mod to see what's up, I recommend Doom: The Golden Souls Remastered. It's good fun.
Aside from the obvious minecraft... Arguably I'd say Factorio. They have a robust, feature-rich modding API built into the game that allows for relatively easy, wide ranging game play mods to be made very stable, and the number of mods has exploded as a result. The base game is amazing, but mods exist that quite literally triple the amount of game play and in some cases completely overhaul it into a totally new game. The support is amazing, and I wish more game companies could operate as efficiently as Wube does.
Stardew Valley is so much better with mods. Less grinding, more fun. I also like the mods for Skyrim and Minetest a FOSS Minecraft-like game.
Just from a percentage standpoint, the Frackin Universe modpack adds so much to the Starbound experience which is otherwise relatively simple and something you only really play through once. There's like two or three extra Starbounds' worth of content, although that can make it overwhelming when starting out
The Sims 4 is basically almost unplayable to me without custom content and mods and community made bugfixes.
Mount and Blade Warband! Base game is just ok, but mods like Diplomacy make it way better. Then you look at Prophecy of Pendor or Perisno and you've got basically an entirely new game with the same engine and it's awesome. I have hundreds of hours of Mount and Blade, and probably only like 25 of them are vanilla.
RimWorld. It's amazing what people can do from QOL to whole new factions or weapons. Amazing and the dev is very helpful during updates to try and not break mod support. Just blown away.
Risk of Rain 2 has a fabulous mod scene, with a lot of ways to make the game more wild - both in terms of power fantasy and in terms of difficulty - as well as modding in playable characters from other games, like League of Legends and Tomb Raider.
Slay the Spire also has excellent mods, so much so that the developers worked together with a mod team to creator a fan-made expansion.
Assetto Corsa. So much new content, of amazing quality.
I'm not sure its fair to say "most improved" but I do believe that Deus Ex is a game everyone should play, but I do not believe it is truly playable without some content mods to get the game running properly on modern hardware.
Mass Effect: Andromeda
I had no idea the game had a modding scene. What sorta mods are out there, and what would you recommend?
I also had no idea, since mods for prior games had basically nothing, but wow, the Nexus page has a lot.
Nearly all the Sims games for me tbh. especially sims 3, seeing as its a unoptimized buggy mess at times.#
Skyrim! The modding community literally saved this game.
Valheim! A million and one mods to revitalize the game experience, and more than anything else the Valheim VR mod makes it an entirely new game! I’ve got 360 hours sunk into it with my 2 friends.
Cities Skylines is 8 year old and released their final DLC just recently. I'm positive their very impressive mod community can keep that game alive for 8+ years more, if Cities Skylines 2 should fail to measure up.
Half-Life 1
Yes, the king of modding! Many hours spent in TFC, DoD and countless other free mods.
CounterStrike started as an Half-Life mod
I really needed mods for The Witcher 3: Wild Hunt or I would have probably never finished the main story.
I had to get the mods that would autoloot and give unlimited inventory space, otherwise I would have minmaxed the game to tediousness by spamming pick-up and sorting through loot to keep the weight limit.
After getting the mods I could just focus on the story and gameplay without worrying if I'd maximised all my looting.
The Steam version of Sonic Adventure is a bad port of a bad port, but just downloading the mod manager itself undoes one of those bads and the Dreamcast Conversion mod undoes the other, and that's not even getting into the crazy stuff people have done like hack Klonoa and their mechanics into the game
Space Engineers the base game is great, but it comes to life with mods.
From simple things like a more immersive way to paint blocks or customised UI to to hole NPC Factions, new Weapons, dekorative Stuff, all the way to hole new physics systems like Water with flotation, Aerodynamics or re-entry heat.
I rarely play my games with mods, this game is one of the few exceptions. I even went so far as to create some very minor mods my self.
Project Zomboid. Lots of mods that add new stuff (cars, weapons) and quality of life improvements like "Has Been Read".
Terraria, is still an excellent game but the Mod loader makes it tons better with plenty of feature mods and quality of life plus it is available from steam so easy set up.
I don't know if improving is the right word, but the amount of transformative mods older games like Doom, Half-Life or Unreal Tournament (and not just shooters ofc) had, was wild.
Team Fortress started as a Quake mod, Counter-Strike as a HL mod, DotA as a Warcraft 3 mod.
Civ 4 had a great modded scene. The Colonization remake/spinoff in particular has a must-have mod in the way of The Authentic Colonization. The main game, though, had loads and loads of incredible mods. My personal favorite was the Ryse series of mods, which tried to more accurately model the rise and fall of civilizations via various mechanics. I have a lot of hours in the random map variant of it, Ryse Rand.
Modding as we know it today really started with Civ (Civ II, to be precise). There were several sharing different mods back then. I had one of the most popular ones for a while, to the point where MicroProse asked to post a link on the official site. The mods were ZIP files with instructions, and nobody had come up with a name for them. I started referring to them as "modpacks", and that stuck. Eventually that was shortened to just "mods". True story!
(FYI you can see here where MicroProse put links to other websites. Mine was listed in 1997, where the wayback machine doesn't have entries.)
Wait, you're saying you basically coined the term "mods?" That's epic!
Interesting how we went from mods being called modpacks to being included in modpacks. I'd say Minecraft is the biggest example of modpacks somewhat overshadowing the mods contained within them. Few modded minecraft players play with just one mod at a time, like you would have back in the Civ days. For the longest time, mod complications (usually known as modpacks, but sometimes as modmods, like MiscMods for Europa Universalis 3) were the exception to the rule.
Looking at Paradox games, the build-in mod launchers originally only supported playing with one mod at a time. This changed around the Victoria 2 HoD days, which supported loading multiple mods at once. You look at Darkest Hour, EU3, and Vanilla Victoria 2, and they only supported loading one mod at a time (ignoring that the Vanilla Victoria 2 mod launcher didn't actually work, but that's neither here nor there.) Mods have really come a long way. I've seen some incredibly ambitious ones, like total conversion mods trying to convert March of the Eagles into a Cold War game and Imperator Rome into a alternate Victoria sequel. Neat stuff, but time will tell if we see results.
Does Tabletop Simulator count? For board game people, mods are the whole point.