I don't know any way to create new folders in DropBox directly but:
You can create a new folder in GoodReader, and then upload that folder to DropBox.
Many apps, like GoodReader, can access DropBox directly to copy files.
For apps that do not support DropBox, check their OpenIn option (if they have it). If DropBox appears you can use it to open the file in DropBox and then upload it.