These will be largely user-oriented features that developers don't need to know about, and which don't break any backwards compatibility requirements, which is why they haven't been released in the developer builds so far.
My predictions for the secret features are:
1) A new Finder, written in Cocoa, and making heavy (but not tacky) use of core animation. It will maintain backwards compatibility with the existing finder library, so it shouldn't break any existing scripts.
2) A new theme - Illumnous - featuring back-lit windows with halos where Aqua has drop-shadows, a variety of new, resolution-independent widgets, and *no* brushed metal (but Aqua will remain available for those who want to keep it).
3) A variety of slick new features that allow better integration of digital hub components (?TV, iPhone, iPod) and .Mac integration.
4) Something that will surprise us all and make Vista look anemic.
Cheers