> WARNING! You are running this program as root!
> It might be a good idea to use the -%U option to change 
the 
> userid:

It won't affect your downloads at all. 

BUT

Running regular programs (like X, Mozilla, graphic mail 
clients..) as root is potentially dangerous, because if a 
serious bug occurs (like attempting to delete /, or other 
dangerous behaviour) it may crash or destroy your system.
httrack is very well written ( :) ) and therefore there 
should not be any risks.. but you never know - running 
programs as root CAN be dangerous.

Look at Windows systems: all programs are generally running 
with high priviledges (administrator, local administrator 
or with windows 9x with full power). And this is precisely 
why you have so many viruses on these systems.