I mostly enjoy hacks that fix games that have either terribly misguided design decisions, unacknowledged critical bugs or glaring omissions.
Under that light, I'll cite a few.
First, the RNG fix for Monster Hunter 3 Ultimate. This fixes the botched RNG routine in the game allowing it to function like all the games before it and the ones after it, with the RNG seeds rerolled properly at each game load. Capcom at the time said they designed it this way, but I don't believe it, they copped out and didn't want to issue patches.
Second, Mega Man X3 - Zero Project v4.8. The most advanced iteration of a patch that does so much good for the game that it singlehandedly removes it from the quagmire of mediocrity it wallows in and elevates it to be closer to its kin by fixing gameplay issues (botched buster mechanics, awful, unusable up dash and that pathetic, distracting shield effect), not to mention the bonus of adding Zero properly and removing the randomness associated with certain events.
Third, Mega Man 7 Refit - A weak buster and pathetically short iframes really bring this otherwise solid game down quite a bit. This hack fixes that.