There is a new, more stable, version at
http://code.google.com/p/perapp
In particular, I no longer do the kludgy thread killing I mention in the first post, and hence it works on ICS.
If there are other per-app configuration options you'd like, let me know. Something I do have on my horizon is per-app CPU settings, but my motivation is low as my own Epic 4G Touch is unrooted (there isn't a way of rooting it that's both safe and legal as far as I can make out).