Q: Reorganize iTunes folder

Back up before you delete things.  iTunes is pretty structured unless you know what you are doing.  You don't give us any specific folder names or contents so it is hard for us to say yes or no, do it.  Old libraries, probably.  They are mostly there for when you transition a version and the transition gets messed up and you need to try again.  Still, in your situation I back up my computer, then try removing items and if something goes wrong I can restore.

What are the iTunes library files? - http://support.apple.com/kb/HT1660

More on iTunes library files and what they do - http://en.wikipedia.org/wiki/ITunes#Media_management

What are all those iTunes files? - http://www.macworld.com/article/139974/2009/04/itunes_files.html

iTunes 9 [and later]: Understanding iTunes Media Organization - http://support.apple.com/kb/ht3847

Image of iTunes folder structure Dec. 2011 - https://discussions.apple.com/message/16923545
see also:
Image of folder structure and explanation of different iTunes versions (turingtest2 post) - https://discussions.apple.com/message/13025536 and https://discussions.apple.com/message/17457605