The thing about what Atari sent is, there is very little detail on what is actually infringing. If a company sends a DMCA takedown notice, which this is despite the jargon, then they need to specify the content that needs to be removed and why. (You work together to remove it).
These letters are nothing more than a shot across the bow in the hopes to scare enough people into closing stuff down. The It seems they took the lazy route and didn't look at the content of pages they deemed inappropriate in the initial cease and desist letters. (lazy lawyering).
Reading through some of the forums where this is discussed,
it seems Atari are at least listening to some site owners and agree they may have been over zealous.
Its pitiful because they are attacking the very fan base that keep them somewhat relevant. I think they have realised they went in with two feet flying when a more tactful approach might have been best.