The reason I didn't use disavow is that I only have two directory links to this site and Google's instructions (when you actually go to the tool itself) are to use it if you have a LOT of backlinks that are problematic. I'm trusting Google's advice there and not using it for two links.
And just fyi, back when I did this in 2004 or so, I was very green and actually had the understanding that the directories were going to send me human visitors, not just Google rankings. Once I saw I wasn't getting any traffic from the links themselves, I quit doing it. I've always been paranoid about avoiding behaviors that smack of "gaming Google" because they always seem to figure it out sooner or later. I just didn't know better at the time, and I'm sure I'm not alone there. There is a lot of bad advice (some with the best of intentions) out there for new, self-taught webmasters and it's easy to make mistakes.