XML for Overlapping Structures (XfOS) using a non XML Data Model by Alexander Czmiel was an interesting paper at the 2004 ALLC/ACH on implementing systems with overlapping hierarchies.
While overlapping hierarchies would seem to be an obscure or advanced issue in markup, I think it is important to opening up markup practices to match existing intellectual practices, especially exploratory practices.
LMNL (Layered Markup anNotation Language) is what Alexander ended up using and his paper provided me an introduction to this fascinating language developed by Wendell Piez. LMNL looks like it could be used for exploratory markup and then built up into sophisticated interpretations of text.
A related paper is: Beyond the “descriptive vs. procedural” distinction that Wendell Piez gave at Extreme Markup Languages 2001 that nicely discusses mimetic and exploratory markup. Wendell, along with Buzzetti and Renear, is taking seriously the need to theorize markup – to take markup seriously as an applied humanities issue. Wendell is also trying to implement ideas.