I tried the "Subscribe to Comments" (v2.1.2) and "Subscribe to Comments Reloaded" (v2.0.2).
I haven't tried all the functionality, but both suffer from a killer problem with Atahualpa (3.5.3 - I'm stuck on this version because later ones disable PHP in the options, and Flyn hasn't got round to adding in shortcodes to compensate for this).
The problem with the Subscribe to Comments plugins is that the links they insert into the comment form all mess up and produce page not found errors.
Has anyone used a subscribe to comments plugin successfully with Atahualpa? If so which one and which version of Atahualpa? Also, any pointers to getting it working would be welcome!