You can generate binary diffs using badiff; the website is
http://badiff.org/
and it is available on maven central. It's BSD licensed, so friendly for both OSS and commercial. The algorithm used is a chunked version of the O(ND) diff described in this paper:
http://www.xmailserver.org/diff2.pdf
The diff format isn't particularly compatible with anything else, but it produces some really good and really small diffs.
The library is pretty fast; on my desktop machine it can generate a diff for two random 50MB input streams in 54 seconds. Hopefully that's fast enough; I think it's reasonably impressive since that's a comparison of two token streams of 50 million tokens each. badiff will take advantage of multiple CPU cores when computing diffs.
disclaimer: I'm the author of badiff, so of course I think it's cool. I'm always open to suggestions; things like being able to read/write "standard" binary diff formats sound like cool new features to add in upcoming releases.