Back in version 6 of the suite you could run the something like the following:
jamf recon –skipApps –skipFonts -skipPlugins
This was identified as a bug, & changed so that recon now always follows the JSS set inventory options.
However, this comes in very handy when deploying apps via self service so that only apps would be reconned. Which would reduce recon time massively.
(i created a feature request for this on 26th June 2010)