The default publication comes with the XHTML Doctype, the Links Doctype, the OpenDocument Doctype and the CForms Doctype.
A tutorial on creating/adding new doctypes can be found here.
The XHTML Doctype is for situations where users ask for complete freedom on what information can be inserted into a document. While this approach doesn't restrict you, it also looses some of the major benefits of well defined document types.
The Links Doctype is mainly to show that Lenya is able to handle arbitrary doctypes but can also be used for link-lists.
The OpenDocument Doctype is a standardized XML-based file format specification suitable for office applications and has been developed by OASIS.
The CForms Doctype is an example of how Lenya manages formular data based on Cocoon's CForms in conjunction with Ajax.