My best recommendation is to always use Google Closure Compiler. By default it doesn't work much better than other minifiers, but there's an --compilation_level ADVANCED_OPTIMIZATIONS flag that can have a dramatic result. To use this, it is likely you'll have to structure your code differently and make sure exports work correctly, but we were able to take reduce a further 50% with this one change. In this release, we also changed a few other flags (in the code itself; there are no command line settings) which we thought would be advantageous to our file and userbase.
We also do a lot of string replacements. I built a simple templating system that glues files together and also can replace descriptive, programmer-friendly, key names with single letter variables. Strings can weigh a lot. In this release in particular, I also looked at the minified JS and examined which strings could be partially combined. For example, "rotateY(0deg)" and "rotateY(10deg)" could both have the "rotateY(" extracted and save some bytes. It matters less if you're using gzip compression, but we can't guarantee that among our users. The key is to make sure this doesn't make the code hard to read or edit in the future, and only tackle the most significant changes.
Not quite related to the HYPE.js runtime, but we also focused on reducing the entire export data size, including the JSON animation info. We again used a lot of string substitution -- "startTime" and "duration" in code simply become "s" and "d". With JSON, depending on the key name you might also not need quotes around them, so for an animation object it could be {s:1.2,d:3}. The quote characters can add up! There's lot of other things we did such as not exporting the common/default values since we could figure this out if the key does not exist, and being smart about element id's so they would not be some long UUID.