I'm following Djibriel's walkthrough, so things like taking Sabin back to South Figaro are covered. There's not too much that would be affected by doing something like that, since the writers anticipated that particular scenario.
I'm not really looking into the sequence-breaking type of stuff that CAN be done, but there are some patches I put in place to prevent the more likely ones, like Shadow Leaving a One-Man Party, or the Airship Game Over exploit. So far I have not seen a patch that corrects the tile in South Figaro that can lead to the break where Celes can be replaced by Kutan the moogle, but I would do that one as well.
Most of my personal changes have been in the menu side of things, like changing names and descriptions of spells, items, enemies and the like. We've already seen what was happening there when I wasn't vetting my changes properly.
