Stenod and those guys can push the stock pcm very far, that's for sure. But I think most other high hp combinations use big stuff 3, accel, or fast with big stuff 3 being the leader of the pack since it has a system specifically designed to work with the stock COP setup and even use all factory style sensors if desired.
I'm running big stuff 3 but it hasn't been fired yet so I can't tell you much more than that...most people use the stock gm truck coils although msd does make a set of aftermarket coils ($$$), just no use using them since the truck stuff and even stock stuff works fine.
The stock coils will take you VERY far. well over 1000+rwhp. Pretty amazing actually. Not sure how the MSD ones work, don't know anybody using those as of yet. We had 6.0l truck coils on harlan's car when it went 170+ in the 1/4.
As far as the tuning stuff.... Big stuff three seems to be the software of choice lately. The guys at W2W have had amazing luck with that and used that software to put an LS1 in the 6's! Seems to be the latest and greatest. For street car stuff, the new MAFT Pro seems to be working very well on kevins car. Eliminates the maf and turns the PCM to reading speed density or something like that. You'll have to forgive me, tuning is for sure not my backround.