Terra used to let me do it, but then it got busted with an update, and after I deleted it and reinstalled it, the option was gone.
The Offline Reader app is nice, just doesn't have the different folder option.
I use Pocket + Evernote to save webpages. Pocket allows me to get a clean version of the webpage (no ads, banners and such) and Evernote provides me the organization capabilities (tags and notebooks). I could save the webpage directly on Evernote but it would come with all the adds so I use Pocket as filter.