GDSII

A defacto standard: the IC mask database developed by the now defunct Calma-the dominant IC layout program of the 70's & early 80's. Calma's GDSII stream is read and written by every IC tool and many MCM & BGA tools. Note that mask making equipment do not read GDSII directly-there is always a translation step into the machine's native instruction code.

DXF, DWG

Actually an ASCII representation of AutoCAD's internal database-not designed at all for mask work, in fact it's downright poor for mask design.  However, AutoCAD's market dominance (millions of legal and millions more of illegal users) make DXF, DWG a commonly used database for mask-generation.

GERBER

GERBER data is the raw data, commonly used to drive mylar film photo plotters. GERBER data is most commonly used to make film for printed circuit boards.

EMASK /DW MANN

Pattern generation data is the raw instructions for a pattern generator-various versions depending on the specific machine. Few software writes PG data driectly-for mask-generation we need to convert the GDSII or the DXF,DWG file to PG data. The PG language and machine operation has some limitations such as vector plotting and flash counts per hour.