The JTS Topology Suite is an API for modelling and manipulating 2-dimensional linear geometry. It provides numerous geometric predicates and functions. JTS conforms to the Simple Features Specification for SQL published by the Open GIS Consortium.
Theba is a plugin-based image analysis framework for segmentation of and measurements on 3D and 2D images. Theba has a nice GUI that allows inspection and manipulation of the image and a wide range of plugins including segmentation.
NESD-Imaging is a 2D rendering framework for Java. It combines JAI and Java2D and extends them by providing lazy rendering (do not block UI). It provides geo-positionned images rendering (à la google-map). It scales well to large image set (>500GB).