Jmol understands a number of output file formats that include information about molecular vibrations including Spartan output and GAMESS .log files.  The display at right is from the file CO2-DZV-hess.log.  To follow along you can use the applet at right or download the file and open it in a copy of the Jmol application.
 
The button below will return you to the initial view of the file when it is loaded. This file was generated by performing a full Hessian calculation in the GAMESS software package on a model of the optimal geometry of CO₂ computed using the DZV (double zeta valence) basis set.

When Jmol loads a file it stores the information about each vibrational mode in a separate "frame"  Within the application you can see which frame and the frequency of the vibrational mode in the information box at the lower left of the image (see below).
The web viewer does not show this information.  You will need to provide it for your reader.  In the image above vectors are displayed.  Getting them to look right can be tricky, so their display is not discussed in this tutorial.  For more information see the Jmol scripting documentation. Limited control of vector display is available in the right-click pop-up menu in the "vibration" submenu.
TO ANIMATE VIBRATIONS turn them on using either the "tools" menu in the application or the right-click menu in either the application or the applet at right.

A WARNING: some pieces of software generate information that Jmol interprets as vibrations for translational and rotational degrees of freedom.  For example GAMESS generates results for all of these.  Thus the first 5 (linear molecules) or first 6 (non-linear molecules) frames are not vibrations.  For example with CO₂ the first 5 are not vibrations.  If you click the button below it will move to frame 3 and turn vibrations on.  Note that this is A TRANSLATIONAL DOF not a vibration.
The first valid vibrational mode in CO₂ is in frame 6.  Navigate there by using the right click menu and selecting model 1.6.  Notice that the vibrational energy in cm^-1 is shown in the menu.  If you have vibrations on your display should look like the one you get by clicking on the button below. This displays an animation of one of the two degenerate bending vibrations at 717 cm^-1.

Selecting model 1.7 with vibrations on will generate the view you get by clicking on the button below. This displays an animation of one of the two degenerate bending vibrations at 717 cm^-1.

Selecting model 1.8 with vibrations on will generate the view you get by clicking on the button below. This displays an animation of the symmetric stretching mode at about 1400 cm^-1.

Selecting model 1.9 with vibrations on will generate the view you get by clicking on the button below. This displays an animation of the assymmetric stretching mode at about 2380 cm^-1.

You may look at any of these intermediate views again by clicking on the appropriate button.