If you are looking to completely separate content from structure and presentation using something like DML, take a look at DML2 (also here on freshmeat.net).
As an example of what it's capable of, its documentation is in 2 forms: multi-part HTML, and single-file text. Both were written using the exact same content file with 2 different templates.
An open, cross-platform journaling program.
A scientific plotting package.