Via this Google story I learned about MapKnitter, an open source tool to upload your own aerial imagery and combine it into a GeoTiff and TMS/OpenLayers map. MapKnitter is aimed at images coming from balloons and kites.
From their wiki: "MapKnitter (MapKnitter.org) is a free and open source tool for combining and positioning images (often from MapMill.org) in geographic space into a composite image map. Known as “orthorectification” or “georectification” to geographers, this step covers the process of figuring out where images can be placed on an existing map, and how they can be combined, or “stitched” together. You are likely to have many images of overlapping or identical areas, which is why MapMill or some type of sorting is used to determine which source images to use from the original set."