Any kind of archiving utility like 7zip, WinZip or WinRAR will allow you to pack the folders into a single file which can be uploaded and then downloaded and unzipped by the recipient. This would be your best method as I don't know of any free sites that allow folder hierarchies.
Just be sure to use the .zip file format when archiving folders as windows 7 and 8 support it natively, but do not natively support file formats like .7z or .rar files so any recipients would have to either also have 7zip or another utility capable of reading those file types in order to unzip them.
http://www.7-zip.org/