When I install the latest ATVFlash, 3.4.3 and start it and run NitoTV settings, I get the choice of H.264 or Perian. It used to be that one of the first instructions from AppleCoreLLC was to install Perian. How would I decide which one to use, H.264 or Perian as it appears to a choice that has to be made.
The choice that you are asking to make is whether to use the Apple supplied QuickTime h.264 codec or the Perian h.264 codec.
From the research that I have made into this it boils down to the complexity of the h.264 files that you are viewing. If you are going to be viewing basic h.264 content created from a non-HD source, such as a standard DVD then the Apple codec should be just fine. However, if you are going to be viewing HD content h.264 or content that uses the high complexity profiles then you will be better off using the Perian codec.
For my purposes, dvd rips made using Handbrake, the Apple codec will suit me just fine.
Hope this helps,