Well, right now the one that comes to mind is the OnDamage event. Osiris has a terrible OnDamage event, but charscripts have a much better one. If you needed to hook into that generically, you basically have no choice except to override base.charscript or defaultcharacter.charscript, which will cause your mod to become incompatible with any other mod that does this.
I've been working around this stuff by using gamescripts and so far it's worked, but I've also seen a lot of screenshots on the forum of people injecting their logic into shared scripts. I suspect many don't know that if you do this, it not only makes their mod incompatible with other mods that edit the same file, but they also need to update those files when patches come out or risk causing reversions.
