For those interested in a command-line version of the Panda Engine here's one you can use. Specially interesting is the switch to turn on/off the Genetic Heuristic Engine (GHE from now on). The most useful ones for scanning samples on disk are:

-nob        Do not scan boot sectors
-nos        Deactivate sounds
-cmp       Scan compressed files
-aex       Scan all extensions
-rpt:        Create report file (ex. -rpt:c:pavclreport.txt)
-heu:1    Activate heuristic scanning paranoid mode
-nomem  Do not scan memory 

Here you can find the win32 version with advanced tracing and logging. Of course this is available for research purposes only. Contact me if you want the linux version or wish to use this for a not-for-profit public service purpose with sig updates.