I agree--the global Javascript disable is pointless in this day and age.
As for enabling it by domain, check out the "noscript" extension. I've been running it for a couple years and it (a) lets you see from which domains a page is loading Javascript files and (b) lets you enable/disable Javascript from particular domains. I've never enabled facebook.com, for instance, since I don't have an account there and I don't like the idea that every page out there with a "like" button is tracking me.
As for enabling it by domain, check out the "noscript" extension. I've been running it for a couple years and it (a) lets you see from which domains a page is loading Javascript files and (b) lets you enable/disable Javascript from particular domains. I've never enabled facebook.com, for instance, since I don't have an account there and I don't like the idea that every page out there with a "like" button is tracking me.