There isn't anything inherently wrong with using a name someone is already using. The issue is whether or not the subsequent user's use would cause confusion in the prior user's markets. Heck, the GNOME Foundation themselves are using a name that was already being used. The Lake County Nursery in Perry, Ohio, registered Gnome as a trademark in 1980, and has used it continuously ever since.
The Lake County Nursery's use is in class 031 (Natural agricultural products), and within that class it is in the area of plants.
GNOME Foundation's use is in these classes and areas within those classes:
IC 009 (Electrical and scientific apparatus):
• downloadable computer software tools and libraries used for the development of other software applications
• downloadable computer software development tools
• downloadable computer software for creating and managing a computer desktop
• downloadable computer software for use as a graphical user interface
• downloadable computer software for word processing, database management, and use as a spreadsheet
IC 042 (Computer, scientific & legal):
• computer software development
• computer software design
• computer programming for others
• technical consulting services in the field of computer software licensing of intellectual property
It's pretty clear that none of those are likely to cause confusion in Lake County Nursery's market, so their using a name already in use was fine.
Here are the classes and areas that Groupon was trying to claim the mark for. They include several areas in the same classes GNOME's are in, so concern on the part of the GNOME Foundation is certainly warranted. On the other hand, trademark classes are very broad (e.g., "Electrical and scientific apparatus"), and Groupon's areas within these classes are fairly far from GNOME's areas, so I can see them actually believing that they were far enough apart to not cause confusion. If it went to a hearing, I could see it going either way.
IC 009 (Electrical and scientific apparatus):
• computer hardware and software for processing point of sale transactions, payment transactions, voucher redemption, appointment scheduling, customer relationship management, customer location detection and awareness, inventory management, analyzing merchant transactions, and for evaluating and managing information on business performance and customers
• computer application software for mobile phones, smart phones, PC tablets, and electronic tablets for processing point of sale transactions, payment transactions, voucher redemption, appointment scheduling, customer relationship management, customer location detection and awareness, inventory management, analyzing merchant transactions, and for evaluating and managing information on business performance and customers
• computer software and hardware that enables users to send and receive pricing, financial transaction, customer information, and payment processing information directly to and from a mobile device and a cloud-based server
• downloadable mobile computer apparatus software applications that enables users to send and receive pricing, financial transaction and payment processing information directly to and from a mobile device and a cloud-based server
• computer hardware, namely, hand-held computing devices in the nature of credit card processing units consisting of electronic machines for reading credits cards, tablet computers for point of sale transactions, payment calculating machines, and magnetic coded card readers and the software used to operate the aforementioned computer hardware
• contact management software used to organize and retrieve customer contact information
• electronic commerce and transaction application software that allows users to engage in electronic business transactions via a global computer network
• printer software for operating printers and printing. accounting software used to track and present financial information relating to sales
• schedule management software used to organize and retrieve scheduling information
• payment systems and devices, namely, electronic card readers, payment calculating machines, magnetic coded card readers, credit card processing units consisting of electronic machines for reading credits cards, point of sale terminals, and multi-functional computer hardware with payment function
• computer hardware, namely, electronic card readers for electronically readable cards
• tablet stands
IC 035 (Advertising and business):
• providing marketplace information, namely, commercial information on merchants, customers, consumer products, and business events and services
• providing business information in the field of point of sale transactions, payment transactions, voucher redemption, appointment scheduling, customer relationship management, customer location detection and awareness, inventory management, merchant transactions, business performance, and customers
• providing a website featuring ratings, reviews and recommendations on products and services offered by merchants, consumer products, business events and services, and business information related to sale transactions, payment transactions, voucher redemption, appointment scheduling, customer relationship management, customer location detection and awareness, inventory management, merchant transactions, business performance, and customers
• business planning and management for marketing, promoting or advertising the goods and services of others
• marketing, promotional marketing, and advertising services
• administration of a customer loyalty reward program to promote the retail services of others for participants to obtain benefits from purchases of a company's goods and services
• appointment scheduling services
IC 042 (Computer, scientific & legal):
• providing use of cloud-based non-downloadable software for processing point of sale transactions, payment transactions, voucher redemption, appointment scheduling, customer relationship management, customer location detection and awareness, inventory management, analyzing merchant transactions, and for evaluating and managing information on business performance and customers
• providing temporary use of non-downloadable software that enables users to send and receive pricing, financial transaction, customer information, and payment processing information directly to and from a mobile device and a cloud-based server
• software as a service (SAAS) services featuring software that enables users to send and receive pricing, financial transaction, customer information, and payment processing information directly to and from a mobile device and a cloud-based server
• providing use of cloud-based non-downloadable software for payment services, merchant analytics, and for evaluating and managing information on business performance and customers
• technical support services, namely, troubleshooting in the nature of diagnosing computer hardware problems and troubleshooting of computer software problems
• installation and maintenance services for computer software for processing point of sale transactions, payment transactions, voucher redemption, appointment scheduling, customer relationship management, customer location detection and awareness, inventory management, analyzing merchant transactions, and for evaluating and managing information on business performance and customers