> I would like to use a file text containing the list of 
these
> Url but I still need a specific 'project name' for each. 
Is
> there a way to associate a project name with each Url in 
a list?
Err nope - you have to run one instance each time. But 
using some scripting it should be okay?
for i in `cat mylist.txt`; do
url=`echo $i|cut -f1 -d ' '`
path=`echo $i|cut -f2- -d' '`
echo "launching httrack for $url in $path .."
httrack <parameters does here> "$url" -O "$path"
done

With the mylist.txt as below:
www.example.com /foo/example
www.example2.com /bar/otherexample

(On Windows you can do the same using the cygwin shell)