The EMOF-based models should be 100% OMG compliant, so you should select this option when you need to interchange models with other OMG tools.
The Ecore-based models are those used internally. These are more efficient since EMOF models incur an overhead through implementation as Ecore models with an EMOF adapter object attached to each Ecore object.
Note that these definitions are independent of the editor file associations defined in the General->Editors->File Associations preferences page.
All text extensions define the extensions for which builders will perform a text (concrete syntax) to XML (abstract syntax) conversion, provided the corresponding nature has been added to the project.
The first text extension defines the extension appended by a reverse transformation to text (concrete syntax) from XML (abstract syntax) conversion.
The first XML extension defines the extension appended by a forward transformation from text (concrete syntax) to XML (abstract syntax) conversion.