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
Visualizing optimized geometries and energies from a Jaguar 5 scan job
Animation of frequencies from a Jaguar frequency calculation
molfreq.py (requires python 3.1)