They've gotten most all of the bigger fish at this point (or they've preemptively closed up shop already). That said, the last big EPA suit I saw (maybe 6-8 months ago) had like 85 businesses listed (most I'd never heard of), so they're getting the smaller ones, too.
The pre-emissions stuff changes the game a little bit, as you're not 'defeating' anything. They could still probably make the argument that by tuning it, you're altering the calibration by which it passed whatever emissions controls, but I haven't heard of them doing that (yet). That argument could technically be made all the way back to changing jets in carbs, but I don't think they'll go that far.
As for the hobbiests tuning vehicles for themselves, I don't think they'll come after individuals. Way too much effort for what they'll get out of it. The better bang-for-their-buck move that they'll make is going after the software and hardware providers. I know they already did this with SCT several years back (forcing them to remove lot of options and tables from the tuning software). It'll be interesting to see what kind of pressure they'll be able to put on the non-US companies.