Molden

Molden is a free visualization program for molecular structures, written by G. Schaftenaar. The official Molden website can be found here

While Molden isn't able to read the plain Jaguar output, molden-compatible files can be created either by Jaguar (keyword ip90=2) for orbital visualization, or extraction from the plain .out file.

Collection of molden scripts:

Visualizing geometries and energies from a Jaguar 5 optimization
exterg

Visualizing optimized geometries and energies from a Jaguar 5 scan job
scanexterg

Animation of frequencies from a Jaguar frequency calculation
molfreq.py (requires python 3.1)