There's a lot of stuff, it's hard to know where to start.
The PS1 FFs, I don't think I'll ever touch the originals again, it'd be like playing some action game on Very Easy. But I already made a thread about it.
Morrowind, there's a laundry list of mods, not a single one. FNV likewise, although it's already mostly fine with JSawyer's mod.
JA 2 1.13. It's been a long time, though, I haven't followed any developments in recent years.
Victoria 2: HPM/HPM+. I've tried a couple of others, but usually go back to those.
I'm playing Far Cry 2 with Tom's Realism Plus right now. There are a couple of other similar mods I haven't tried. Simply superior to the vanilla game, removing things like constant outpost respawn, bullet sponge enemies and other annoyances, while adding some very cool features.
SMAC: Thinker mod. Much better AI, which means better game.
MoM: Caster of Magic. Very extensive overhaul. I don't agree with every change, and MoM is not obsolete because of it, but I think it's generally better, with better balance and more viable strategies.
MGSV: Ultimate Phantom Pain Mod. Very similar to Infinite Heaven, which may have surpassed it in recent years. I like increasing the guards' sight range while scaling up the effectiveness of camo to create a nearly perfect stealth experience.
GTAs: there's lots of stuff, even some intersting looking difficulty mods for 3 and VC that came out recently that I haven't played. I'd at least check out the reverse engineered projects, they're more stable than vanilla and allow you to tweak a lot of settings.
Certainly a lot more that I'm forgetting.