A while back I posted on the painfully poor choices in creating thumbnails of JPEG2000 files. Since then I’ve come to realize that support for image file processing in Java is even worse than I’d realized. Now I’m trying to make thumbnails from TIFF files. At first I went with JAI, even though it hasn’t been supported for five years and relies on implementation-dependent classes. I’d done this before successfully, but now I’m trying to do it in an EJB under JBoss. This runs into a NoClassDefFoundError trying to get com.sun.image.codec.jpeg.JPEGCodec. A web search suggests there’s some obscure trick necessary to access com.sun.image, but I couldn’t figure it out. It occurred to me that for what I’m doing, javax.imageio should be sufficient to do the job. It can read an image file, standard Java classes can scale the BufferedImage it produces, and then it can write the scaled image to a file.
Only one trouble: javax.imageio knows nothing about TIFF. A search on imageio and TIFF leads to suggestions to use JAI.
Really, what kind of language is that poor in dealing with common image formats?
Mad File Format Science 
Have you taken a look at ImageJ [1]? Though it is a primarily a GUI based Image Processing Application, it can also be included as a library. It has native support for many file formats [2] and even more through plugins.
I hope this helps.
Tom
[1] http://rsbweb.nih.gov/ij/
[2] http://imagejdocu.tudor.lu/doku.php?id=faq:general:which_file_formats_are_supported_by_imagej