I finally found a program that I've been dreaming of for years. Image Analyzer will perform lossy compression on PNGs, preserving the alpha transparency of the PNG file while, in most cases, creating a file comparable in size to a JPEG.
Originally I had hung my hopes on JPEG 2000, which supported alpha transparency as part of the updated JPEG file format. However, application support for the new format never coalesced, and 11 years past the release of the standard it still isn't supported by Firefox or Internet Explorer.
Back to Image Analyzer… Loading a PNG with alpha-transparency into the program will trigger a dialog which asks whether it should "Merge alpha channel with picture?". Choose No to load the alpha channel and RGB data as separate images, then choose the RGB image and choose "Save As" from the File menu. From the save dialog, click the "File format option" button on the right-side of the dialog. Click the "Alpha transparency" checkbox and choose the correct alpha channel from the dropdown that appears. Then choose the compression quality from the slider at the bottom of the dialog. The default quality setting is lossless. I've found a setting of about -7 to be a nice balance between the size of the file and the quality of the output. The "Test" button allows for previewing of each quality setting to find what works best for each image.
The program works like a charm, and the output looks great. This saved my sanity while working on a new gradient-and-dropshadow heavy website that refused to cooperate with my attempts to flatten the images. PNGs again ftw.
