Already mentioned:
X3 Zero project
Starforce DX
DS castlvania patches
I am surprised no one mentioned the X5 and X6 tweaks yet. honestly makes both games so much more enjoyable I refuse to play vanilla X6 anymore. I think they absolutely stand up with the rest of the series with these patched. the N's Edition Megaman X7 is also an improvement, but let's be honest... no patch is truly saving that game.
I also need to mention the Final fantasy 5 patch that let's you remove attack and items to allow you to set up to 3 unique skills (4 on mime and freelancer)
considering how many skills you get on jobs that are sort of pointless one offs (like the dragoons lancet, a skill I honestly really like) it's a super fun mod just for seeing what silly stuff you can come up with.
I love every one of those.
Except Star Force.
And Castlevania but if I liked Castlevania after the GBAs, I would probably use the Portait of Ruin patch that doesn't change the portraits.
Don't want 'em ruined.
I guess everybody but you spaced on the Megaman X5 and X6 improvement & tweaks patches. Personally, I use my own X6 from the Tweaks Patcher, 'cause I don't like what they changed Rainy Turtloid's weapon for Zero to, something like triangle in the air? Pfft, stupid. I wanna use it on the ground and spam it over and over!
I also like choosing each updated portait for every character, trying to make it as close to canon as possible.
The Three Slots patch for FFV is a necessity, it makes the game so much less bland when you have options that actually let you combine multiple class skills. I have my own version of FFV with multiple patches such as Three Slots, and some other, small QoL patches for preference/balance; for example, I never liked the patches that let you always see hidden passages, or always be able to sprint, because it makes Thief practically irrelevant, and at that point you may as well make a custom class to replace it altogether. Also I prefer the original translation, not the official one but the one off RHDN.
Hold onto your BUTZ