Javaview a pure java implementation of advanced 3d features that actually works and is fast! For comparison minecraft uses opengl for all its 3d - however, Notch then went on to work on a pure java (afaik!) shooter http://0x10c.com/ but development has stalled apparently.
Honorable mention in this category: http://jmol.sourceforge.net/
octave is now (since the 3.8 release) seriously offering a replacement for its default gnuplot (slow, restrictive!) interface: an opengl plotting option that uses fltk for cross-plattform windowing. Compilation of octave takes very long though.
Consider this: octave is a scripting language for numerics and gnuplot is a scripting language for plotting. The octave-gnuplot interface works by converting octave to gnuplot. That has certain limitations in regards to speed and responsiveness. Fingers crossed the 3.8 release and beyond resolves this.