Binding of Isaac is very improved by mods. Also, even if it's more plugins than mods, but every MMOs have a lot of plugins to custom the interface and make it more efficient for the type of gameplay you want
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All of them. I personally find Oblivion totally unplayable unless its been heavily, heavily modded, other games in the TES aren't as bad. I suspect that's why those games still have active communities is because of modding.
All of the older Grand Theft Auto titles were saved by modding originally (ignoring the remade definitive edition trilogy of course) GTA III, GTA Vice City, GTA San Andreas, and even GTA IV were all released for older hardware and much different technology at the time they were released, so there's some weirdness getting each of the games to run without issues or well on modern hardware and modern Windows. GTA IV specifically has a notoriously bad PC port that is at times hard to play without any mods or community made utilities.
All four games are substantially better with mods, from small things like restoring the original soundtracks for each of the games that have since been patched out due to licenses expiring, improving performance and stability, bug fixes, and even things like widescreen support. (Original GTA San Andreas specifically looks amazing with widescreen support and some other mods throw in)
My favorite mod currently is the GTA IV downgrader, found on GTAForums, it downgrades the version of your game, making it compatible with all of the most important utilities and mods made by the community.
For me it's Zelda games.
Ocarina of Time for 3DS on Citra in gorgeous with the HD Texture packs https://www.henrikomagnifico.com/ and you can also grab PS4 buttons to make it more playable and the motion controls with the PS4 controller are actually good.
The stutter and low quality on Breath of the Wild and now Tears of the Kingdom were unbearable for me, but BotW is phenomenal on Cemu and TotK is running on most computers at over 30fps, even in 4K, and my PC has a really nice processor in it and rarely drops below 60fps at 4K.
I didn't make it very far, but the Dolphin version of Skyward Sword using the thumbstick for sword instead of the crappy Wii motion controls was SOOO much better. I'll probably go back and finish that after I beat TotK.
Edit: oh, and the most important part of emulating those games is actually being able to set the attack/action buttons to something normal, like the playstation cross button instead of the Switch A / PS Circle. I love Nintendo games, but hate their stupid button layouts.
I'd say it is definitly not any TES game. While the engine and released tools give amazing modding capabilities, it is still fine without mods. Back in the day, I spend 800 euro on a videocard just to graphically mod Skyrim. And I have no regrets. But I just as well regularily play on the Switch curreny, as I van continue on the train. Similarily I still booted Oblivion on my PS3 a while back. I feel TES games improve with mods, but aren't tge worst without.
Now for a game that "nééds mods" rather "thas great modding capabilities" I would say the first that comes to mind for me is Mugen. That old fighting game game with 1 stage and 1 character out of the box, but thousands of community made characters, stages, and new character select screens. It caused some videos of the ridiculous (in the best way) fights in a time YT was mainly weird but fun.
Beat Saber. It wasn't saved by mods, but almost any serious player will have a number of them installed to dramatically improve the experience. #beatSaber
I would say the binding of Isaac. The game is amazing but I now really struggle to pay without some quality of life mods
Seconding Rimworld, but even without mods it is an amazing game with easily 1k+ hours of gametime. My favorite mods are QoL mods, or ones that add additional flavor to my colonists. If I could only pick a single mod to install, ever, it would be Common Sense.
Outside of Bethesda and Minecraft, the other one that comes to mind is The Sims. More of a niche following, but for those that love deleting pool ladders, mods are necessary for happiness, flavor, and adding actual challenge.
A few off the top of my head: StarSector, ARMA, Monster Hunter (both World and Rise) and L4D(2). All of them are solid game already but modding adds so much value to an already good game.