I think this is a genuine mistake, although Kristen Keller seems to be acting on behalf of Atari, Inc. she clearly has no evidence of direct violation of copyright, the cease and desist letter is more like a 'generic accusation'. The letter includes this:
Based on available information, Atari has a good faith belief that the url(s):http://dcemu.seanbajuice.com/dcemu-atari800.htmhttp://dcemu.seanbajuice.com/dcemu-DC7800.htmhttp://dcemu.seanbajuice.com/dcemu-dcs2600.htmhttp://dcemu.seanbajuice.com/dcemu-lynx.htmhttp://dcemu.seanbajuice.com/dcemu-stelladc.htm
infringes its copyright and other intellectual property right by copying, reproducing and/or offering for distribution, display and/or download (including through links to other sites) unauthorized console emulation software and/or unauthorized copies of game products (software) protected by Atariâ€™s copyright rights. Atariâ€™s copyrighted works that have been infringed include:
Atari 800; Atari 2600; Atari 7800; Atari Lynx
Kristen Keller has implied that the url(s) contain "unauthorized console emulation software and/or unauthorized copies of game products (software)". There does not appear to be any software in either of those url(s) which is copyrighted by Atari. The Atari 800, Atari 7800, and Atari Lynx emulators are useless without the BIOS files - and they ARE NOT included in the downloads. The Atari 2600 does not have a BIOS so all the 2600 emulators can be released as fully working, they can also include PD ROMS (unless some of the ROMS contain copyrighted characters, graphics, sounds, etc.). As for the emulators themselves being classed as unauthorized, that is true, but it DOES NOT make them illegal in any form unless they contain copyrighted code (which they DO NOT) and/or are being distributed as official Atari software (which they ARE NOT).
With regards to any possible copyright infringement, Christian Groessler's README for Atari800DC says this:
As for the name ATARI, the cease and desist letter states:
Atari is a global producer, publisher and distributor of interactive entertainment software for all market segments and all interactive game platforms. Atari is the exclusive owner of intellectual property rights, including copyrights and trademarks, in numerous interactive entertainment software products, including those listed below, and vigilantly protects its rights.
Kristen Keller has pointed out "trademarks" (see above), however, the cease and desist letter makes no further mention of trademarks, and no mention of any trademark violation, only 'Infringing Material'. The letter does however clearly state "Atariâ€™s copyrighted works that have been infringed".
Back to the name: ATARI only appears with one emulator - Atari800DC, an easy compromise would be to rename the thing A800DC. Trying to abolish the Use of the ATARI name within webpages (titles or otherwise) would be a pointless and extremely costly exercise, a recognition of trademark ownership would probably be the least requirement for webpage legalities: "Atari is a trademark of Atari, Inc. blah, blah, blah, this site is not affiated with blah, blah, blah, this emulator is not endorsed by blah, blah, blah."
Now the tricky bit - Logos and artwork. StellaDC has 'themes' and if you look here...http://svolli.org/software/dcstella/images.html
...you'll find the ATARI name, logo, and some modified fonts. These are arguably 'fan art' and could possibly fall under 'fair use' but that's an entirely different legal minefield. Anyone remember SONY v BLEEM?, at one point a mere screenshot of a game caused controversy (and mounting debts due to legal proceedings), but BLEEM was a commercial product and we are talking about freeware emulators on a dead console here.
To round up all this rambling, I'm sure a clear and concise email to Kristen Keller would sort this matter out with very little hassle, final quote from the cease and desist letter:
This notice is not intended to be a complete statement of the facts or law in this matter. Nor is it intended to be a complete statement of Atari's positions, rights or remedies, legal or equitable, all of which are specifically reserved.
If you have any questions, please contact me by phone 212-726-6500 or email at email@example.com
SVP & General Counsel