How to zero fill a virtual disk’s free space on windows for better compression?

On windows use the sysinternals tool sdelete to zero out all the empty space. The command you want would look like this sdelete -z c:.

Usage: sdelete [-p passes] [-s] [-q]  ...  
sdelete [-p passes] [-z|-c] [drive letter] ...  
-a         Remove Read-Only attribute.  
-c         Clean free space.  
-p passes  Specifies number of overwrite passes (default is 1).  
-q         Don't print errors (Quiet).  
-s or -r   Recurse subdirectories.  
-z         Zero free space (good for virtual disk optimization).

For Linux I suggest you use zerofree.