what about using a textfile containing all links instead of 
single links? you could use the "replace"-function of any 
text editor to insert the user and pass like this:

<http://www.host.com>

replace //www ---with---> //user:passs@www

<http://user:pass@www.host.com>

and it's done for all links! whttrack will use authorisation 
with all links