The plugin Landmark Correspondences calculates a transformation between two corresponding landmark clouds and renders a transformed image. The landmarks are read from point selections over two images. The transformation is estimated by a least squares or Moving Least Squares fit for the available models.
TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized datasets.