calibre 0.5 does not have support for MOBI indexing (that's what is responsible for the waypoints and joystick based navigation on the Kindle). calibre 0.6 however does, thanks to some nifty reverse engineering by Gregory Riker.
As for support for special mobipocket markup, it should be possible to add support for it to calibre, however, it's not really a priority for me, since most calibre users will never use it. Still if someone wants to take it on, I am always happy to accept patches.
