> I was wondering if there was an easy way to import a 
whole 
> folder of favorites and then have HTTrack download all 
the 
> contents of all the sites within the folder.

- Drag & drop the bookmark.html file to the "Web 
addresses:" winhttrack window
- Select "Download all sites in pages (multiple mirrors)"

> Also, is there an easy way to organize downloaded sites 
> into folders and subfolders and have HTTrack generate one 
> index file for all the folders and subfolders?
Not yet ; this is on the TODO list, but this won't be 
implemented soon