> For example, I would like to backup 
> <http://www.ticalc.org>, which is a HUGE site (in case 
> they go down sometime, like adcritic.com did)
> But, I already backed up <http://www.ticalc.org/pub/>, 
> which in itself is 700 megs of the site

You can use filters, such as:
-* +www.ticalc.org/* -www.ticalc.org/pub/*

BUT in a *NEW* project (because if would erase the pub 
folder) - this may not what you need here

-OR-

select your existing project (with only the pub 
folder), and select 'Continue an interrupted mirror' 
(NOT 'Update'), and CHANGE the URL (example:start from 
the top) and if necessary the filters (such as 
+www.ticalc.org/*)

A new project will be built, BUT all previous files 
will be kept, because the engine will use the previous 
HTTrack cache.

Anyway, **backup** your project FIRST, or a mistake 
could wipe out everything (which is generally 
annoying, especially when you downloaded a lot of data)