... it depends, are the files in the many mp3 folders named the same thing, like "track01" no matter what folder they are in, like most of my mp3s which are organized by Music/bandname/album? if not, then what you can do is right click the main music folder, left click search, for the "all or part of the file name" type in *.mp3" if they are all mp3s or do *.wma if the are wma files, this will turn out a list of all files, regardless of name, that are mp3 files. in the window with all the files showing, just press "ctrl+a" to select them all, then drag them to the "big folder" you created, this will move all the mp3 files to one big folder instead of many folders. if there are any duplicates, it will ask if you want to overwrite. compare filesize, etc. to figure out if they are really duplicates.
if you did what i did, you have thousands of mp3s under folders organized but its by "track##" then you need to download 1-4a name
http://www.1-4a.com/rename/ to rename the mp3s in each folder by bulk so you can move everything to one big folder.
or you can just buy a bigger HD, then use bootitng or norton's ghost to copy the entire partition or drive from your current HD to a larger one...